The geological diversity of Raja Ampat forms the wealth of habitats in the area, both terrestrial and marine. This is what makes Raja Ampat has mega-biodiversity and various types of endemic flora and fauna that cannot be found anywhere in the world.

For that reason, 66% of Raja Ampat's terrestrial area is a Nature Reserve or CA with 7 land conservation areas covering an area of 399,564 hectares consisting of CA Waigeo Barat, CA Waigeo Timur, CA Misool, CA Batanta, CA Salawati, CA Kofiau, and CA Torobi .

Terrestrial Biodiversity

Identified 9 terrestrial habitats spread over the 4 main islands of Raja Ampat, contributing to biodiversity of endemic fauna and flora that are still well preserved and naturally. This is what makes more than half of the Raja Ampat area become conservation area.

The terrestrial biodiversity of Raja Ampat is as follows. About 874 plant species that 9 are endemic and 6 are protected species, of which 360 species are trees. Also there are 114 species of herpetofauna with 5 species of which are endemic and 5 other species are protected. There are also 47 species of mammals, of which 1 is endemic and 3 is protected. And lastly, there are 274 bird species with 6 species of which are endemic and 8 species are also included in the protected category.

Marine Biodiversity

The Coral Triangle or commonly known as the World's Coral Triangle Region is an area of nearly 4 million square miles covering the oceans and coastal waters of Southeast Asia and the Pacific that surrounds Indonesia, Malaysia, Papua New Guinea, the Philippines, Timor Leste and the Solomon Islands. This area is home to the greatest marine biodiversity on earth. It is home to 75% of the world's coral species and about 2,500 fish species. This biodiversity and environment is formed by the complexity of geology and volcanic activity known as the "Ring of Fire".

Indonesia became part of the Coral Triangle Region when its declaration was also signed by President Susilo Bambang Yudhoyono at the World Ocean Conference (WOC) on May 15, 2009 in Manado. And, the location in this area has earned Raja Ampat the nickname "The Heart of Coral Triangle".

As the heart of the world's coral triangle, this marine area has unrivaled wealth, including: 540 hard coral species (more than 75% of the world's coral species); 60 types of crayfish; 1,070 types of reef fish; 699 types of soft animals (mollusks). This is the reason why the water conservation area in Raja Ampat is so wide, both regionally and nationally, which is then grouped into 5 areas.

The 5 Regional Water Conservation Areas or KKPDs cover an area of 1,125,940 hectares, namely: the Dampier Strait KKPD; Mayalibit Bay KKPD; Ayau-Asia KKPD; Kofiau KKPD and South East Misool KKPD. In addition, there are also 2 National Water Conservation Areas or KKPN covering an area of 185,000 hectares, hereinafter referred to as Aquatic Nature Reserves or SAP which consists of the West Waigeo Islands SAP and the Raja Ampat Islands SAP.

The complexity of Raja Ampat's underwater geology also creates underwater caves that have their own aesthetic value. Underwater caves and fracture channels as well as seeps that connect these caves make this area one of the best diving spots in the world.

In addition, the discovery of a living fossil, namely the Raja Laut fish or Coelacanth (extinct 66 million years ago) where the remaining two species in the world are found in Africa and North Sulawesi, were also found in Raja Ampat on July 2 2018.