Raja Ampat is in Papua in Indonesia. The name given to these islands comes from a local myth. The four major islands found here are Waigeo, Misool (which is home to ancient rock paintings), Salawati, and Batanta.
Flying from Jakarta/ Bali to Sorong, with connecting flights in Makassar or Manado are offered by:
Commonly, divers/visitors will join a liveaboard, stay in a diving resort, or stay in a homestay during their visit to Raja Ampat.
Liveaboards leave from Sorong, and take guests around Raja Ampat. To access the diving spots, they use small rubber boats with a few divers.
Most diving resorts offer pick up from Sorong by private speedboat. If not, visitors going to North Raja Ampat can take the Ferry from Sorong to Waisai (the capital city of Raja Ampat). The ferry leaves every day at 14h00 from Sorong City, and arrives at Waisai around 16h30. From Waisai, visitors will be picked up by their resort's diving boats. They must make sure they contact their resort before arriving to Waisai. To get to the diving spots, resorts use their own diving boats. If guests want to visit any island on their own, they have to rent a boat.
In order to get to the Homestays, visitors should take the ferry from Sorong to Waisai, and arrange a pick up service from their homestay. There's no public ferry to get to the islands where the homestays are. If guests want to visit the area, they have to talk to their homestay owner, and arrange a trip with his own boat.
Before going to a dive spot, divers need to obtain a permit from the local Papua police station. Guests need to bring their passport and three copies of the passport page with the Indonesian Visa. The diving organizers can help them with these formalities.
In Raja Ampat, you can see different types of fish and corals. Raja Ampat is the place where coral species reach 75% of all known species and fish nearly 1,300 species.
The Raja Ampat islands are a truly natural phenomenon with enormous biological diversity. The amazing marine landscape means that underwater photography should be on the top your list during your stay.
However with Raja Ampat’s natural conditions, high endemic level of land, sea biodiversity, coastal ecology, and local culture & tradition the islands offer more than just amazing landscapes to photograph.
So you may also consider:
On North and West Waigeo, you can see a traditional bamboo flute (suling tambur) performance. This traditional performance usually takes place during religious festival, on Independence Day, (August 17th), and during visits from important officials or leaders. If you are interested in anthropology, this is something to definitely consider in your agenda.
In East Waigeo, particularly in front of Urbinasopen and Yesner villages, there is a very interesting and unique natural phenomenon, which can only be seen every year-end. A light comes out from the ocean and wanders around on its surface for about 10 – 18 minutes. After that, it disappears and can only be seen again at the following years-end. Local inhabitants in both villages call this phenomenon the “Sea Ghost”. This is more than just a sunset view, overlooking from your liveaboard.
In Tomolol, you'll be amazed by the caves in the area, where you can see paintings of huge human palms and animals which were painted by ancient cave dwellers. While on North Waigeo, you can also take in some history with a visit to the World War II caves where the Dutch and the Japanese army built bunkers. The locals will sometimes perform a war dance. There is also the ever-flowing waterfall of Salawati, which is a sight you should not miss.
You may rent a small boat if you wish to stop and make personal discoveries along the line of the beaches. As the Raja Ampat Islands have four mountainous main islands and hundreds of small islands in their vicinity, you may want to take this opportunity to explore. In addition, the Karst area is a beautiful and original natural phenomenon, as it has various unique flora and fauna as its attractions e.g., Bird of Paradise (Cenderawasih) Botak, Red Cenderawasih, Maleo Waigeo, Kus-kus, orchids, palm etc. You can also trek around the islands to find hidden beauties, like waterfalls and ancient caves.
In addition, there are also exotic locations such as the Ayau islands consisting of small islands on a very large atoll. Many islands in this archipelago have white sands with a large seabed connecting one island to another. But there are also islands with unique sands that the local community calls “zandplaat”, which are a unique habitat for local vegetation. On these islands, mothers and children of local tribes collectively catch sea-worms (insonem).
For diving enthusiasts the favorite destination is usually South Waigeo. But while you are here, why not take the chance to visit Kabui Bay with many karst islands, goa tengkorak (cave of skulls), and the historical sites of Raja Ampat in Kali Raja. You can see a variety of birds in Yenwaupnor and Sawinggrai village, the Salay dance in Saonek, and plaited handicrafts in Arborek. In Arborek, visitors can dive and watch groups of stingrays. In Sawandarek, there's a white sand beach with sea ducks and beautiful corals. In addition, there is a traditional village where you can walk around in and enjoy the unique slow paced atmosphere.
You can also dive in West Waigeo, Batanta, and Kofiau. These potential destinations are great places to visit by houseboats. The Karst islands in Wayag, especially, have very interesting natural attractions to enjoy.
Dining services are provided by the diving organizer, and range from an international menu to fresh traditional food made by the local people. Naturally, there will be a variety of seafood dishes. Do try the fish soup. There's a local specialty called Sup Ikan Kuning (Yellow Fish Soup), served with local spices.
There's three different types of accommodation in Raja Ampat: the liveaboards, the homestays and the diving resorts.
The homestays are eco-resorts built using traditional materials owned by the local villagers with basic rooms and affordable prices (around 50 USD per person per night). All of them offer the accommodation, the food, tea/coffee and drinking water. Some of the homestays have a diving center run by the owner, or a relative of the owner. Most of the Homestays are in North Raja Ampat (around Waigeo Island), but there's a few in Batanta and Misool Islands as well.
The Diving Resorts are owned by foreigners or Indonesian businessmen. They offer Bungalows or rooms at higher prices than the homestays (from 60 to 350 USD per person per night). All of them offer full board stays with diving (optional). Most of the resorts are around Waigeo Island (North Raja Ampat). A couple of them (Misool Eco Resort and Papua Paradise) are in Misool and Batanta Islands.
source : http://wikitravel.org/en/Raja_Ampat