Where to dive in Indonesia?

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I agree also, however lembeh probably offers the best and widest selection of macro subjects that is easily accessible. Obviously Ambon and areas in PNG also offer great macro, even komodo and RA,but I don't think I would say don't bother with lembeh. It's cheap and easy to get to and for macro lovers shouldn't really be missed. Reports of bangka island diving have also been very positive. Bali also offers some great varied diving from mantas,molas and great reefs of lembongan to liberty wreck to secret bay etc.. It's not all just about Komodo, Alor and RA. Infact some friends of said recently that Komodo was aces but RA was not a good as expected. Maybe go off the beaten path and try halmahera or lease islands.
 
Dived on the Liberty wreck near Tulamben last week and really enjoyed it, really good coral and stacks of marine life - early morning dives are best, far less people!!
 
Wakatobi has been the best managed dive resort i've been too. Mostly macro.

Palau is nice, i've always dove with Neco Marine. Lots of ppl dive with Sam's as well. FYI don't bother eating out at the restaurants if you are staying at the hotels, food ain't all that great.
 
Raja Ampat, around the Dampier Straits, is great for mantas, both giant and reef in season, black-tip reef sharks, some white-tips, wobbegong, and schooling fish. December to April best for giants, September to late May for reef mantas. There is excellent diversity here, on one reef the world record for the highest number of fish species counted on a single tank dive was set in 2012. One week with unlimited diving starts at $1850. Komodo is very good, there are basic but decent liveaboards from Labuan Bajo starting at $150 per day for three to four dives and all meals in a fan-cooled cabin. If there are four of you you can charter one with AC for $220 per person per day Komodo liveaboards - Indigo Safaris

You can combine both in a couple of weeks - here is a link to some galleries from a recent trip there (February 2013) 10 days in Raja Ampat and five in Komodo Bartlett Images - Christopher Bartlett's Blog
 
If you go Palau I would recommend eating at kramers however. Food is decent, the hammerhead hot wings are great! If first time indo maybe combine lembeh and Bali and do Palau as well. Will give u hit of everything!
 
A month will allow you to cover the best. First, I wouldn't bother with Palau. For the most part, everything in Palau, Indonesia has better. The exception would be sharks, but they are better and easier places to photograph sharks than Palau. I would also rule out South Sulawesi, i.e. Wakatobi. Again, like Palau, good macro and wide angle, but better in other parts of Indonesia.

The best wide angle would be a Raja Ampat itinerary, followed by Komodo. There are lots of macro opportunities throughout Indonesia, with Lembeh being the most famous and popular. The first time we were there, there were only 4 dive operators. The last time was a bit more crowded, more like 4 boats at every dive site.

The best bang for your diving time is to pick a nice boat and do 2 itineraries back to back during the transition trips from Raja to Komodo or the other direction. This would be either fall or spring. Example, do a Sorong to Ambon trip. You will get your wide angle fix early on. Then do the boat's next trip from Ambon to somewhere further west. You will have a day or so in between to dive the muck and macro of Ambon. You will get more reef and coral, but still more macro from Ambon heading west. Wherever the second trip ends, you then fly to Bali. Spend 2 days diving in Tulamben and a few days exploring Bali without a housing around your camera. Go home well rested.
 
Just to point out to the OP, Palau, although it does boast amazing diving, is NOT part of Indonesia... I would definitely look to dive Palau, but maybe not on the same trip as Indonesia, as travelling between the two might be difficult to schedule...
 

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