Ambon
Critter Heaven. The Twilight Zone at Laha in Ambon harbor in Maluku province really is a must do muck dive. The site offers a wide range of macro creatures, frog fish, some bat fish, many moray eels and a shoal of scatfish. The pier and its surrounding is full of interesting macro live. There is also a fairly big wreck lies in the bay of Ambon.
Bali
One of the most beautiful islands in the world, Bali is Indonesia's most popular dive holiday destination. There are big pelagic dive sites for Manty rays and Mola mola.The USAT Liberty wreck is one of Bali's most famous dive site. And some of the best muck divesites for Mandarinfish, seahorses, ghost pipefish, frogfish, sea slugs, octopus etc.
Forgotten Islands
They extend from Timor to West Papua in a magnificent landscape far from any hustle and bustle of metropolitan areas. These volcanic islands offer some of the best and still largely unexplored dive sites in the Indonesian waters. Clear, Deep blue waters, endless reefs, spectacular walls of and colourful coral.
Halmahera
The Coral reefs are rich with colourful combinations of hard and soft Corals. Be delighted by the ever present schools of Anthias, Wrasses, majestic Angelfishes, and larger predators - Reef Sharks and giant Trevallies. Macro life is really interesting, finding many species of nudibranches, some of them not even catalogued yet.
Komodo
Komodo National Park was established in 1980 and was declared a World Heritage Site by UNESCO. One day you can be crawling along the bottom looking at pygmy seahorses, frogfish and unusual nudibranch and the next you are in the big blue on an open water pinnacle as the mantas fly by, the sharks circle and the dolphins hunt, and the next day diving a live volcano.
Raja Ampat
Located off the northwest tip of Bird's Head Peninsula on the island of New Guinea, Raja Ampat, or the Four Kings, is an archipelago comprising over 1,500 small islands. There are some areas where soft corals and sea fans dominate, others with amazing diverse hard corals, seagrass beds, mangroves, shallow reefs, drop offs, caves, black sand, white sand.