MISOOL, Indonesia — There is an explosion of color beneath the surface in Raja Ampat, a remote archipelago in eastern Indonesia where sharks, mantas and sea turtles glide alongside vast schools of fish through sea fan coral formations, some of which are only found in its waters.

“There’s nowhere on Earth that has as many fish, corals and everything else packed into one small place,” said Mark Erdmann, an American coral reef biologist who has spent more than two decades studying the region and became a central figure in building Raja Ampat’s conservation model.

The world famous diving archipelago sits at the heart of the Coral Triangle, in southwestern Papua, where powerful ocean currents carry nutrients that sustain what scientists describe as the most biodiverse marine ecosystem on the planet.

Long regarded as a global model for ocean conservation, Raja Ampat ecosystems are now under pressure, as concerns grow over the expansion of nickel mining alongside a surge of international tourism.

The reefs didn’t always look as healthy as they do today. In the early 2000s, fishermen from other parts of Indonesia and Southeast Asia used explosives and large nets, damaging corals, decimating shark populations and forcing local residents who relied on fishing to travel as far as 10 kilometers (6 miles) offshore for a catch.

During those years, the government depended on mining and forestry as the region’s main economic drivers.

That trajectory began to shift in 2023 when a marine assessment by Conservation International sparked conversations between local leaders and environmental groups on how protecting Raja Ampat’s waters could deliver food security and lasting tourism revenue, while safeguarding one of the ocean’s most critical ecosystems.

“We brought some leaders to visit more developed areas such as Bunaken and Bali with the hope that they could see for themselves up close the benefits of natural resource management,” said Syafri Tuharea, a conservation expert who heads the Raja Ampat Marine Conservation Area.

Those exchanges laid the groundwork for 10 marine protected areas established from 2007, covering a 2 million-hectare (4.9 million-acre) area, including 45% of Raja Ampat’s reefs, seagrass beds and mangroves.

Today, local communities patrol the waters, enforce fishing rules and monitor tourism activity, largely financed by tourism revenues, including from a 700,000 Indonesian rupiah ($40) marine park entry fee.

After two decades of protection, the results are significant. A 2024 report from the Misool Foundation, one of the islands under the marine protected area, found that fish biomass has risen by 109% — a measure that serves as an indicator of ecosystem health.

The same waters now host 2,007 documented reef mantas, a large number considering the species is vulnerable to extinction because of overfishing across much of the Indo-Pacific ocean.

This conservation success is unfolding alongside a broader transition to renewable energy, a shift that is rapidly increasing demand for nickel.

The government granted new nickel mining concessions in 2025 on three northern Raja Ampat islands, some within a declared UNESCO Global Geopark and near top dive sites.

Nickel is a key component in electric vehicle batteries and essential for building wind and solar infrastructure. It has become central to Indonesia’s economic development — the country holds about 43% of the world’s reserves, according to the U.S. Geological Survey.

Mining has fueled tensions within communities, where residents depend on fishing and tourism, both of which could be jeopardized.

Following a public outcry last summer, four concessions were revoked, but one remains on Gag Island, where mining started in 2017.

“The heavy machinery, excavators, bulldozers — they’re still there (in the islands),” said Timon Manurung, director of Indonesian environmental group Auriga Nusantara.

He said that no one is taking responsibility for repairing the damage already done.

The environmental risks of nickel mining are amplified by the geography of the islands, which are steep and receive heavy rainfall, conditions that can send sediment from mining sites directly into the sea.

“In the end, it will cause coral reefs to die,” said Tuharea, the marine park manager.

The affected zone also sits along a critical migration corridor for reef manta rays, one of the archipelago’s biggest tourism draws.

Beyond its marine richness, the region also contains extensive seagrass meadows and mangrove forests — coastal ecosystems covering only 0.1% of the ocean floor and 1% of the global tropical forests, according to the U.N. Environment Program. These function as powerful natural sinks to absorb carbon dioxide and help regulate the climate.

A study in March by Manurung’s environmental group found that deforestation has already reached nearly 1,000 hectares (around 2,500 acres).

“It might not seem much for Indonesia, but it is a lot for small islands,” he said.

On viewing decks overlooking Raja Ampat’s Waigeo Barat islands, visitors from France, Spain and the United States watch boats sail between shades of turquoise and blue.

Visitor numbers have held steady over the past decade, but the profile of those arriving has shifted dramatically. Foreign tourists now dominate visits to Raja Ampat, accounting for 95% of roughly 42,000 annual visitors. Domestic tourism has declined by more than two-thirds in the past decade, according to data from the Raja Ampat Regency.

International tourists are far more likely to travel on liveaboard boats for weeklong diving trips. These have rapidly increased over the past decade, according to Kristanto Umbu Kudu, who has guided divers through these waters for 25 years.

Conservationists say this is adding growing strain on reefs through anchoring, as well as waste and sewage discharge.

“Our data shows that in 2024, there were 218 tourist ships,” Tuharea said. “Can you imagine how many square meters of coral reef will be destroyed because of the anchors?”

Authorities are now considering mooring systems and restrictions on boat numbers.

At Blue Magic, one of the archipelago’s top dive sites, once crystal-clear waters are now filled by pink jellyfish tangled in waste.

“That’s something which still breaks my heart every time I see these big rafts of floating plastic,” Erdmann said.

For divers who have explored reefs around the world, Raja Ampat still stands apart. Pol Ramos, a Spanish marine biologist and co-founder of Odicean, a project that combines ocean education with dive expeditions into the region, said that its ecosystems are truly remarkable.

“It is one of the few places in the world, alongside the Amazon, where biodiversity actually increases from year to year,” he said.

Raja Ampat is home to about 75% of the world’s known hard coral species and more than 1,700 species of fish, according to Erdmann.

But what is at stake isn’t only the loss of ecosystems, but also the genetic diversity they contain. Every species carries millions of years of evolutionary information encoded in its DNA, which Erdmann describes it as nature’s library of solutions.

“As we go into a more and more uncertain future with climate change,” Erdmann said, “it’s that genetic diversity that’s what we have to work with in terms of how we adapt.”

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