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What makes these waters a cauldron of life? "Habitat, habitat, habitat," says biologist Mark Erdmann, senior adviser to CI's Indonesian Marine Program. "Extensive fringing reefs, wave-pounded drop-offs, calm deep bays funneling upwellings of nutrients, sand flats, mangroves, sea grass meadows—all in an area that's isolated and still for the most part intact."

How these reefs became, in Mark's words, "a species factory," goes back geologic lifetimes to when a series of ice ages lowered ocean levels, leaving small, isolated seas in which species could evolve and diversify. Now the region is a crossroads for Pacific and Indian Ocean species, whose numbers are still being counted. Surveys in 2006 revealed marine life rivaling Raja Ampat's richness—and at least 56 new species—just to the east along the island of New Guinea around Fakfak and Cenderawasih Bay. To encourage protection of these sites as well as Raja Ampat, CI, the Nature Conservancy, and the World Wide Fund for Nature–Indonesia, with the backing of the Indonesian government, created the 70,600-square-mile (183,000 square kilometers) Bird's Head Seascape. Most of it is not yet legally protected, but the government this year named seven new marine protected areas covering nearly 3,500 square miles (9,100 square kilometers) in Raja Ampat.

What the Bird's Head Seascape holds: 2,500 islands and reefs, nearly 1,300 fish species, 600 coral species, 700 mollusks (including seven species of giant clam), sea turtle rookeries, and more. What it's been robbed of: sharks. They've been slaughtered by outside commercial fishermen supplying the shark-fin soup market. Commercial fishing remains a threat, as does logging and nickel mining. Blast fishing by local subsistence fishermen has damaged some reefs, though the practice is fading as villagers become economic partners in conservation programs.

Raja Ampat is the seascape's crown jewel. Fittingly, the name means "four kings." Centuries ago those kings were men, four rajas granted rule here by a sultan of the Spice Islands, today's Moluccas, just to the west across the Halmahera Sea. Now Raja Ampat's four largest islands are considered the kings. Their waters make them truly royal.

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