Indonesia Liveaboard Cruise Destinations

The most famous cruise destinations in the Indonesian island archipelago

Indonesia Liveaboard Cruise Destinations

Spectacular Underwater World

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Indonesia is a country of geographical extremes, and without doubt the world’s most complex single nation, comprising of 17,000+ islands stretched over 5200 km from Banda Aceh, on the tip of Sumatra in the west, to the remote highlands of West Papua in the east.

Of those many islands three – New Guinea, Borneo and Sumatra – are among the world’s largest, only 6,000 actually have names and less than 1,000 are inhabited.

New Guinea in the east, is the world’s second largest island (after Greenland) and is divided roughly 50/50 with Papua New Guinea, with Indonesia having the western half (West Papua) and the eastern half forming the mainland of PNG. While Borneo, the third largest island in the world, is shared with Malaysia and Brunei, with the lion’s share of about 73% belonging to Indonesia and forming the provinces of Kalimantan.

Indonesia Liveaboard Cruise Destinations

Read below interesting information about the offered Indonesia Liveaboard Cruise Destinations
throughout the Indonesian island archipelago based on high demand of divers, snorkelers and explorers.


The most famous Indonesian Liveaboard Cruise Destinations

Komodo Archipelago
Raja Ampat
Kalimantan (Maratua, Kakaban,Sangalaki)

Alor & Banda Sea
Forgotten Islands & Halmahera
North Sulawesi (Bunaken/Lembeh)
South/East Sulawesi (Wakatobi)






Komodo Archipelago
(Rinca, Komodo National & Marine Park)

is a national park in Indonesia located within the Lesser Sunda Islands in the border region between the provinces of East Nusa Tenggara and West Nusa Tenggara. Komodo is part of the Lesser Sunda chain and forms part of the Komodo National Park. It lies between the substantially larger neighboring islands Sumbawa to the west and Flores to the east. The island’s surface area covers 390 square kilometers. Komodo Island is home to the Komodo Dragon, the largest lizard on earth.

Komodo (Indonesian: Pulau Komodo) is one of the 17,508 islands that comprise the Republic of Indonesia. The island is particularly notable as the habitat of the Komodo dragon, the largest lizard on Earth, which is named after the island. Komodo Island has a surface area of 390 square kilometers and a human population of over two thousand.

The people of the island are descendants of former convicts who were exiled to the island and who have mixed with Bugis from Sulawesi. The people are primarily adherents of Islam but there are also Christian and Hindu congregations.

Liveaboard dive & exploration cruises depart by most operators from Labuan Bajo or Maumere / Flores. The Komodo National Park is definitely one of the highlights to dive and cruise in the Indonesian Archipelago and because of its relative easy accessibility one of the most demanded dive and cruise destinations in Indonesia also because of the world famous Komodo Dragon lizard which can be observed in the National Park areas by visitors.

indonesia liveaboard cruise komodoThe Komodo Marina Park offers a great variety of  fishes, superb and untouched coral reefs, big fishes hunting actions, and pelagic fishes at every dive site will make your dives unforgettable.

Komodo is also known for its population of manta rays, it earns its reputation not only for the majestic rays, but also of its abundance of marine life and huge populations of corals. The best way to hit all of these top dive spots in Komodo is to go on a liveaboard for at least 3 days (but preferably 7) so you can reach the further out dive spots that aren’t accessible on the main land.

The park includes the three larger islands KomodoPadar and Rinca, and 26 smaller ones, with a total area of 1,733 km2 (603 km2 of it land). The national park was founded in 1980 to protect the Komodo dragon, the world’s largest lizard. Later it was dedicated to protecting other species, including marine species. In 1991 the national park was declared a UNESCO World Heritage Site.

Komodo National Park has been selected as one of the New7Wonders of Nature. The waters surrounding Komodo island also contains rich marine biodiversity. Komodo islands is also a part of the Coral Triangle, which contains some of the richest marine biodiversity on Earth.




(Mt. Kelimutu, Volcano exploration cruise)

Flores (Indonesian: Pulau Flores) is one of the Lesser Sunda Islands, a group of islands in the eastern half of Indonesia. The population was 1,831,000 in the 2010 census and the largest town is Maumere. The name Flores is derived from the Portuguese for “flowers”.

Flores is located east of Sumbawa and Komodo and west of Lembata and the Alor Archipelago. To the southeast is Timor. To the south, across the Sumba Strait, is Sumba island and to the north, beyond the Flores Sea, is Sulawesi.

Diving Komodo National Park is an exciting affair but does require a bit of diving experience as the area is known for its swift and powerful currents. Water temperature here ranges from 73-82˚F (23-28˚C) with the colder temperatures mostly in the south.

indonesia liveaboard cruise flores

Divers usually make a beeline for Komodo National Park which can be accessed from the town of Labuan Bajo. Diving around Maumere involves trips to islands like Babi Island, Adonara Island or Lambata Island for sloping reefs, walls and boulders. There are also current filled drop-offs and of course, good muck diving around the bay.

The best time to dive here is the dry season which starts from April and extends to December. Similar to Komodo, this area requires some diving experience because of the currents and choppy surface conditions. Visibility at Maumere averages at about 50ft (15m) only while at Komodo it can be beyond 100ft (30m).

The best way to dive Komodo National Park is on a liveaboard diving vessel and the best season for diving is during the dry months of April to August. That said, some liveaboard vessels run trips throughout the year here.




Raja Ampat

Papua is the largest and easternmost province of Indonesia, comprising most of Western New Guinea. Papua is bordered by the nation of Papua New Guinea to the east, and by West Papua province to the west. Since 2002, Papua province has special autonomy status, making it a special region. Its capital is Jayapura.

Diving in Cenderawasih Bay National Marine Park allows you to experience one of Indonesia’s newest and most exciting diving destinations. Cenderawasih Bay liveaboard trips offer you the unique opportunity of spending hours diving or snorkeling with multiple Whale Sharks. The area also boasts an incredibly rich history from the many battles between Allied and Japanese forces in the area during WWII and the area is littered with dive able wrecks of aircraft and ships. Finally there are the unique biological aspects of the bay.




Raja Ampat & Misool

Located off the northwest tip of Bird’s Head Peninsula on the island of New Guinea, in Indonesia’s West Papua province, Raja Ampat, or the Four Kings, is an archipelago comprising over 1,500 small islands, cays, and shoals surrounding the four main islands of Misool, Salawati, Batanta, and Waigeo, and the smaller island of Kofiau.

The Raja Ampat archipelago is the part of Coral Triangle which contains the richest marine biodiversity on earth. Most of the archipelago is in the Southern Hemisphere with a few small islands northwest of Waigeo such as Sajang Island in the Northern Hemisphere. Some of the islands are the northernmost parts of the Australian Continent.

misool liveaboard divingThe island of Misool in southern Raja Ampat is the second largest of the Four Kings and its surrounding waters has some of the best diving in all of Raja Ampat – with several of the reefs in the south-eastern archipelagos so good, many consider them to be the best in the world!

Located some 150km south-west of Sorong in the Ceram Sea, Misool is a remote and sparsely populated area with no airport, major towns, roads or significant infrastructure.

Getting there usually involves an overnight journey by liveaboard or, if you are lucky enough to be staying at Misool Eco Resort, about 5 hours in their private speedboat.

The interior of the main island is rugged, heavily forested and uninhabited as the small population of less than 10,000 people are scattered around the coastline in about 15 main villages.

The dynamics of that small population are quite interesting as they are split into two fairly distinct groups, but share Misool’s unique language, with the first grouping consisting of those who used to live in the interior of the island and are now mainly Christian.

Distinctively Papuan in appearance – having the characteristic frizzy hair, dark skin, flat noses and wide mouths – they live a subsistence lifestyle from farming and hunting inland.

The second grouping are those who have always lived close to the coast and have traditionally mixed with people from Maluku to the south and have the straight hair, softer features and lighter skin of the Malukans. They are mostly Muslim and rarely venture in land, having always make their living from the sea.

Misool and its archipelagos cover a total area of around 2,000km², with the highest point being on the main island and reaching close to 560m.

Probably the most defining feature of Misool are the spectacular and largely uninhabited islands of its two eastern archipelagos – Sagof-Dalam to the north and the Southern Archipelago to the south.

Their karst limestone composition means some incredible shapes have been created by the ages and their setting in the clear waters of the Ceram Sea makes them visually stunning.




(Sangalaki, Kakaban, Maratua)

Pulau Borneo, (Indonesian: Kalimantan) is the third-largest island in the world and the largest in Asia. At the geographic center of Maritime Southeast Asia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra.

The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south. Approximately 73% of the island is Indonesian territory.

In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo’s land area.

indonesia liveaboard cruise kalimantanA little more than half of the island is in the Northern Hemisphere including Brunei and the Malaysian portion, while the Indonesian portion spans both the Northern and Southern hemispheres. Antipodal to an area of Amazon rain forest, Borneo is itself home to one of the oldest rain forests in the world.




Alor & Banda Sea

Extending at the east- most tip of Flores Island, still in the province of East Nusatenggara, Alor is a name pinned to the regency, the archipelago, as well as the main island of the archipelago. The Alor Archipelago comprises 20 islands and 17 sub-districts and is a great and famous dive location in the archipelago.

The Banda Sea (Indonesian: Laut Banda) is one of four seas that surround the Maluku Islands of Indonesia, connected to the Pacific Ocean, but surrounded by hundreds of islands, as well as the Halmahera and Ceram Seas. It is about 1000 km (600 mi) east to west, and about 500 km (300 mi) north to south.


The liveaboards in the Banda Sea give you a unique once in a lifetime opportunity to explore this rich area with exciting marine life. A dive liveaboard is also the only way to explore the islands. The diving varies around the islands and you will be able to see some great muck diving sites, some sites that attract big pelagics like hammerhead sharks, great wall dives, and beautiful coral gardens.

Thus, a liveaboard holiday in the Banda Sea is very exciting as each dive site and dive area is different from another. Due to its remoteness, the area is not crowded and often your liveaboard will be the only one at a site leaving the reefs to yourself. The liveaboard choices in the Banda Sea are plenty.





Diving in Ambon is focused on the famous ‘muck’ sites of Ambon Bay. These sites are concentrated along the north coast and an incredible variety of unique critters lie the hidden on the gentle slopes – some found nowhere else in the world. Close to the airport is the Laha area, named after a small coastal village. Here, the ‘Twilight zone’ is home to Rhinopias, frogfish, ghost pipefish, different species of unusual octopus, crustaceans and nudibranchs galore.

Amongst the legs of the jetty and amidst piles of debris thrown overboard from fishing boats are schools of striped catfish, silversides and moray eels, whilst Ambon scorpionfish and devil scorpionfish lie camouflaged. Further away are equally interesting sites – Rhino City, Mandarin City, Middle Point and more, all home to unusual and fascinating species. Whilst some of the diving is ‘muck’ to the extreme, these sites are some of the most consistent for sightings of unusual critters in the world. 

For photographers, these sites along the north coast of the Ambon Bay are amongst the best in the world for shooting unusual species. The guides working at the resorts have developed an understanding of the behaviour of many of the species found here and can guide photographers and help them work through their wish list of species. Much like at Lembeh Strait in Sulawesi, Ambon Bay is a place where lovers of the weird, the wonderful, and the bizarrely beautiful will want to come again and again.

Ambon also has some great reef diving along the south coats, particularly at Pintu Kota and Hukirila Cave. These sites offer the potential for a great day trip and respite from the relentless critter hunt of Ambon Bay. For those interested, there is also the wreck of the Duke of Sparta closer to Ambon’s main harbour.




(Forgotten Islands & Halmahera)

The Maluku Islands or the Moluccas are an archipelago within Banda Sea, Indonesia. Tectonically they are located on the Halmahera Plate within the Molucca Sea Collision Zone. Geographically they are located east of Sulawesi, west of New Guinea, and north and east of Timor. The islands were known as the Spice Islands due to the nutmeg, mace and cloves that were originally exclusively found there, the presence of which sparked colonial interest from Europe in the 16th century.

Scuba diving in Halmahera is not only exceptional but also extraordinarily varied: wrecks in Ternate, emerald waters and schools of fish in Tidore, vertiginous and pelagic walls in Bacan, drifting dives in the Patinti Strait, not to mention its beautiful coral gardens.

The islands stretch between the Philippines, Sulawesi, and New Guinea and are connected to the open Northeast Pacific Ocean.

Halmahera is the largest island in the whole Maluku Islands. Tropical, it is covered with lush forests. Everywhere majestic volcanoes come out of a calm sea and the deep forests of Halmahera have remained intact. Its pristine beaches of white sand and coral reefs offer exceptional conditions for scuba diving, snorkeling, and snorkeling. In addition, several outdoor activities can be considered, although to this day it is the underwater world that the visitor seeks.

Located in the heart of the Coral Triangle, its marine ecosystem and rich biodiversity, with exceptional flora and fauna is still a secret gem with so much to be discovered.

Halmahera islands is an outstanding scuba diving destination and is still preserved from mass tourism. In particular, sailors and scuba divers enjoy visiting this remote part of the world and exploring its raw and unspoiled nature, pristine landscapes, secluded bays, and deep and colorful seascapes.

All these splendors are still totally confidential. It is frequent that we are alone on-site during most of our cruises. Halmahera is quickly brought to become known as one of the best diving destinations!




North Sulawesi
(Manado, Bunaken Marine Park, Lembeh, Bangka & Sangihe Islands)

…is a province of Indonesia. It is located on the northern peninsula of the island of Sulawesi, on the Minahasa Peninsula, lies south of Philippines and southeast of Malaysia. It borders Philippines to the north, the Maluku Sea to the east, Gorontalo to the west and the Gulf of Tomini to the south. The province’s capital and largest city is Manado.

Manado is among the highlights of diving in Indonesia and has earned plaudits throughout the world. When you’re scuba diving in Bunaken National Marine Park you’ll witness some of the highest levels of biodiversity in the world, with outstanding fish variety and world-class walls. The clear, warm waters contain astonishingly high numbers of species, whether corals, sponges or fish.

The park is located just out of Manado Bay in the Sulawesi Sea, off the northern tip of Sulawesi, and features some 2 dozen diving sites spread across an area of 75,000 hectares and the 5 islands of Bunaken, Siladen, Manado Tua, Montehage and Nain.

Explore the deep waters of Bunaken from your choice of dive resort and you can see 7 times more genera of coral than Hawaii, 33 species of butterflyfish and over 70% of all fish species known to the Indo-western Pacific.

Oceanic currents sweep past Bunaken Island bringing a steady supply of nutrients. It’s a sure certainty that where there is plenty of food in the sea, there will be an abundance of marine life, and you can be here to witness this rich harvest too. From the smallest commensal shrimp to black tip reef sharks and eagle rays, there is something for everyone in this very special dive destination.

Manado is very popular with fun divers and marine biologists both of whom can take great pleasure from the diversity of coral and fish found here. You will surely encounter marine life here that you have not come across elsewhere.

The most notable recent find within the park was in 1997, when the coelacanth was discovered living in the lava tubes of Manado Tua. This ‘living fossil’ fish brought international media attention to Bunaken Island. Unusual mammals that can be seen include dugongs, which feed on the sea grass beds in the south of the park, and sperm whales, which travel through the area on their way to calve in the Sangihe Archipelago.




South East Sulawesi  (Wakatobi)

Wakatobi is located in Indonesia, in the Southeast of Sulawesi Island. It is a small archipelago of 4 islands called Wangiwangi, Kaledupa, Tomea, and Binongko. These exotic islands offer some of the best diving in Indonesia. Yet not a lot of people know about these pretty islands …

The coast of Papua New Guinea is home to some of the world’s most spectacular diving – dubbed as the ‘underwater photographer’s paradise’, with many international award-winning photos being taken in PNG waters.

Wakatobi offers excellent Scuba Diving on some of the most pristine Reefs on the planet. The resort is located in the Wakatobi National Park (also known as Tukang Besi National Marine Park) in the Banda Sea.

The main attractions here are the outstanding Coral and the amazing Biodiversity. This place is famous for the high density and variety of small creatures and critters you can find. Several new species have been found around Wakatobi.

indonesia liveaboard cruise wakatobi

Serious macro Underwater Photographers come here from all over the world to get excellent pictures opportunities. You can spot Pygmy Seahorse on a superb Sea Fan, rare and colourful species of Nudibranchs and newly discovered species of the Ghost Pipefish.

Wakatobi is not really the best spot for big fishes and action, not like diving in the Komodo National Park for example, but you can still spot many Blacktip Reef Sharks, Whitetip Reef Sharks as well as Grey Sharks on several dive sites. Eagle Rays and Turtles are common encounters too.

The house reef just in front of the Bungalows is known to be as one of the best dive site in the world and you will have unlimited shore diving! Moreover, this is an excellent place for night diving.

You can also explore this underwater world on a Liveaboard trip (Pelagian Liveaboard). I usually use this website to book in advance my liveaboards in Indonesia as they usually have the lowest rates I find. I like it because they have an easy booking system.


Cendrawasih Bay

Home to the largest marine park in Indonesia, Cenderawasih Bay is a far-flung and hard-to-reach destination relatively new on the diving scene. And while it may not match neighboring Raja Ampat for mind-blowing biodiversity, Cenderawasih Bay still boasts an enviable catalog of marine life and is quickly gaining a reputation as the go-to destination for awesome whale shark encounters. 

The immense Cenderawasih Bay is home to the largest marine park in Indonesia and is the only place in the world where it is possible to see such a large number of whale sharks and with such ease, and not only by diving, but simply by snorkelling or swimming. The many Japanese shipwrecks strewn across the bay since WWII are another important call.

A consistent population of whale sharks daily frequent the local fishermen platforms -called “bagan”-, attracted by the fishing of “ikan puri”, small fish similar to sardines, of which they are greedy. The bagans are make-shift floating platforms built from giant bamboo canes, that are then anchored for long periods areas deemed to be rich in fish.

On the seabed of the Gulf of Dore, near the town of Manokwari, are numerous Japanese shipwrecks sunk during the Second World War. Currently there are 6 wrecks open to divers, with the other wrecks either sat too deep for exploration or not yet located. The Manokwari Wrecks are covered in corals and home to an enormous variety of sea life. Inside the boats and on the decks you can still see cases of grenades, ammunition, helmets, bicycles, bottles, pots, pans and plates, etc. On some of the wrecks you can visit the machine rooms and the radio station. The largest ship wreck in the Manokwari Gulf is the Shinwa Maru, a huge 120m long cargo ship that is relatively intact.

Until recent times, the Cenderawasih Bay remained isolated and cut off other seas. This natural phenomenon prevented the exchange of larvae with other seas and the evolution of a large quantity of species endemic to the region. It is also interesting to note that many fish that would normally live in very deep seas, are found living Cenderawasih Bay in relatively shallow waters. The reefs and underwater walls of Cenderawasih Bay are teaming with macro marine life, from pigmy seahorses to needle ghost fish, colorful shrimps and rare crabs. The hard corals are particularly colourful, and sponges are often found on the walls.


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