1) Pulau Weh, Sumatra; 2) Sangalaki, East Kalimantan; 3) Bunaken Marine Park, Sulawesi; 4) Lembeh Strait, Sulawesi; 5) Raja Ampat, West Papau; 6) Ambon, Maluku; 7) Wakatobi,  Sulawesi; 8) Alor – Lesser Sunda Islands; 9) Komodo National Park, Flores and 10) Lembongan, Bali

Here’s our selection of the top diving spots in this vast archipelago which is made up of more than 17,500 islands which stretch over an area more than 5,000km in length

1) Pulau Weh – Sumatra

A garishly colored rhinopias

This volcanic island at the northern-most point of the Indonesian archipelago at the tip of the vast island of Sumatra is where the Indian Ocean meets the Pacific. It has a wonderful range of diving with more sites regularly being discovered and while it is not as well known and the infrastructure is not as developed as some areas, it has a wild, untouched vibe. A bit like Bunaken 30 years ago. Best to visit during the April to November dry season.

2) Sangalaki – East Kalimantan

3) Bunaken Marine Park – North Sulawesi

The reefs around Bunaken have been a marine park since 1991

The islands of Bunaken and Siladen are off the city of Manado on the northern tip of Sulawesi. They are surrounded by high-energy walls and rolling coral gardens which have some of the most exhilarating drift dives through forests of soft and hard coral and crowds of reef fish. Turtles abound and sharks, eagle rays, and other pelagic predators all revel in this protected zone. You can stay in the resorts surrounding Manado and enjoy a 45-minute commute out to the reefs, but far better is to stay in the small but wonderful dive hotels on either Siladen or Bunaken.

4) Lembeh – North Sulawesi

Veined octopus emerge at dusk in Lembeh to hunt in the muck and rubble

Two hours’ drive and a short boat ride from the North Sulawesi capital Manado is the island of Lembeh, and the associated straits between island and mainland are renowned for their amazing muck diving. A large percentage of the critters you will find there will be unique to the region and, in fact, you may not realize that some of them are actually living creatures until the guide points them out. Most of the dive sites are only a short boat ride from your resort of choice and slack currents, shallow water, and the colorful sea life contrasted against the black sand make Lembeh a macro photographer’s paradise. Diving is year round, but peak time for critters is probably July and August.

5) Raja Ampat – West Papua

Pygmy seahorses are frequently found in the gorgonians which abound on the reefs of Raja Ampat. Photograph Maja Stankovski

Raja Ampat – ‘the four kings’ is an archipelago of more than 1,500 small islands of which Misool, Salawati, Batanta, and Waigeo are the largest. According to some marine biologists, Raja Ampat may be the most biodiverse marine habitat in the world with over 1,500 species of fish and 550 types of coral – around 75 percent of all known species. From sharks and mantas, dugongs and leatherback turtles to the minuscule pygmy seahorse and fish in some of the largest schools found in the oceans, Raja Ampat has to be top of the list for diving in Indonesia – if not the world.

6) Ambon Bay – Maluku

An exquisite mandarin fish

Ambon Bay is fast becoming one of muck diving top destinations with underwater photographers ticking off blue-ringed octopus, wonderpus, flamboyant cuttlefish, rhinopias, and mating mandarin fish. There are some reasonable reefs and walls to the eastern side of this long protected bay and the  Duke of Sparta a short boat ride out is a world-class wreck which has hardly been explored.

7) Wakatobi – Southern Sulawesi

A healthy Wakatobi reef. Photo Walt Stearns

Wakatobi is an extremely isolated dive resort in the heart of the Tukangbesi archipelago off the southern tip of Sulawesi. You fly in on a light aircraft and can explore some of the most pristine reefs on the planet from the luxury of a purpose built dive hotel. The house reef is a world-class dive in its own rights and there are nearly 40 other stunning sites to explore. This is an underwater photographer’s paradise with some of the most vibrant and biodiverse reefs on the planet. Dynamite fishing and other dubious practices had taken their toll over the years and the amount of large pelagic life might not compare with other areas but growing conservation awareness is improving that and the sheer quality and beauty of the reefs more than compensates.

8) Alor – Lesser Sunda Islands

Lionfish stalk a reef in Alor. Photograph Maja Stankovski

The island of Alor is towards the remote eastern end of the Indonesian islands. Best dived from a liveaboard for that reason, the location remains mostly unspoiled by human activity and offers a wide diversity of wildlife and diving. Schools of hammerheads are frequently sighted, as are pilot whales and dolphins. Currents on the reef can be strong and so some experience is required, but there are sheltered spots which, due to the volcanic nature of the island and the resulting black sandy sea-bottom makes Alor an excellent place for both muck-diving with macro lenses and wide-angle shots of the bigger stuff. Diving is year round but the best is from September to November when the currents are at their strongest.

9) Komodo National Park – Flores

10) Lembongan – Bali

A diver and a large southern mola (Mola ramsayi)  in Crystal Bay

Nusa Lembongan is one of three islands approximately 30 minutes by speedboat from Sanur harbor in Bali. Most of the diving actually takes place around the larger island of Nusa Penida, famous for sightings of the southern mola at Crystal Bay and the resident population of reef manta at feeding and cleaning stations along the southern coastline. The islands are prone to large swell and big currents, although by and large they are fairly easy to manage – even for novices – through good diving practice and sound dive center planning. Although the islands can be dived on a day trip from Bali, it’s much better to make the journey to Lembongan to take advantage of the earlier access to the dive sites. Aside from the manta and occasional visits from other large pelagic, there is plenty of macro for the keen-eyed photographer, it’s just not always easy to stay in the same place long enough to photograph them!