Sheltered reefs fringe the islands
It is in a remote archipelago off Indonesia, close to the coast of Papua Province, in the Malacca Sea.
The scientists have just submitted a report which estimates that more than 1,100 species of fish inhabit the area, along with 600 species of mollusc and 450 different species of coral.
The diversity of sealife among the Raja Ampat islands is described by the study's lead researcher, Dr Gerald Allen, as staggering.
Diverse species
The Museum of Western Australia researcher identified a record 283 species of fish in a single dive.
And his colleague, who had just completed the authoritative three-volume work on corals of the world, immediately stumbled across seven new species at Raja Ampat.
"As far as the fishes go, it was absolutely mind-boggling," Dr Allen told the BBC.
"Our survey ran for roughly two-and-a-half weeks and over that period I recorded 972 species, which is just phenomenal."
The extraordinary diversity of life in the area stems from the archipelago's position at the crossroads of oceans. The waters mark a meeting point for species from the Philippines, Papua New Guinea and western Indonesia.
Under threat
BBC correspondent Roger Harrabin, who this week dived among the reefs, says the area is also flushed with cooler waters that help to protect the corals from bleaching when temperatures rise during El Niño events.
But the scientists warn that even these reefs are coming under threat from illegal fishing and illegal logging, which leads to soil erosion and silts that eventually choke the living coral.
The charity Conservation International, which sponsored the Raja Ampat expedition, wants the islands made a world heritage site.
Images copyright of Conservation International