JARDINES DE LA REINA, July 14 ― The 6-foot Caribbean reef shark came out of the water thrashing, and Fabián Pina Amargós and his crew quickly pulled it into the research boat.

A team set to work, immobilizing the shark’s mouth and tail, pouring water over it to keep it breathing and inserting a yellow plastic tag into a small hole punched in its dorsal fin.

“What is its condition?” Pina’s wife, Tamara Figueredo Martín, asked.

“Excellent, the condition is excellent,” Pina said, before the team pulled out the hook, carefully lifted the shark up and tossed it back into the ocean.

A marine biologist and director of Cuba’s Centre for Coastal Ecosystem Research, Pina has spent much of his career studying the abundance of fish and other wildlife in this archipelago 50 miles off the country’s south coast, a region so fecund it has been called the Galápagos of the Caribbean.

He has a deep love for its biological riches: the lush mangrove forests, the sharks and grouper, the schools of brightly coloured snapper, grunts and angelfish and the vibrant coral reef, largely untouched by bleaching or other assaults, a bright spot in an often depressing litany of worldwide oceanic decline.

As a student at Havana University, Pina took part in the first oceans survey in Jardines de la Reina (Gardens of the Queen) after the Cuban government established a 367-square-mile marine preserve here in 1996, tightly restricting tourism in the preserve and banning all fishing except for lobster, an important part of Cuba’s economy.

He has completed many other studies since, demonstrating, for example, the beneficial effects of the preserve on fish populations inside and outside the marine sanctuary. And research by Pina’s centre played a role in the government’s decision to designate a marine protected area of about 830 square miles in 2010.

Jake Kritzer, a scientist who works with the Environmental Defence Fund, snorkels over sea grass in the Jardines de la Reina, a protected area in Cuba July 14, 2015. — Picture by Todd Heisler/The New York Times

But Pina still has a long list of questions he would like to pursue. For example, he is eager to learn more about the biology, travel patterns and habits of sharks and Atlantic goliath grouper here, large, highly mobile predators that are important to coral reefs and a major tourist draw. And he hopes someday to understand why the reef in Jardines de la Reina is so resilient, when other reefs around the world are dying, succumbing to overfishing, pollution, coastal development and the effects of climate change.

Conducting marine research in Cuba is not easy. The country has only two principal research vessels: the 30-foot Itajara, the boat used by the recent expedition, and another, larger boat belonging to Havana University.

Travel and communication barriers often make collaborating with American scientists complicated. Microscopes, fishing gear like nets and hooks, refrigerators for storage, cameras and GPS are in short supply. And even mundane necessities like rope must be carefully rationed and frequently repaired.

“The blockade, what you call the embargo, has had a huge impact, especially in environmental science,” Pina said.

Dan Whittle, left, a lawyer with the Environmental Defence Fund, and Jake Kritzer, a scientist with the organisation, look through a bird guide at a research station in the Jardines de la Reina, a protected area in Cuba July 14, 2015. — Picture by Todd Heisler/The New York Times

Like other researchers, he hopes that the recent warming of relations between Cuba and the United States will spur more scientific collaboration and exchange, a critical step for two countries whose ecosystems are closely interconnected, the environmental successes or missteps of one affecting the health and productivity of the other.

“Our two countries are connected by the water, and fish and other organisms move freely there,” said Jorge Angulo-Valdés, a senior scientist at Havana University’s Centre for Marine Research who is also doing work in Jardines de la Reina and has collaborated with Pina. “They don’t need a visa to come down or go up.”

Warblers migrating south from New York take a needed break in Cuba’s Zapata Swamp. Sharks and manatees travel back and forth. Grouper eggs spawned here are eaten weeks or months later as adult fish in Miami Beach.

“When you have two areas that are 90 miles away, it’s not only possible but it’s probable that a considerable number of eggs and larvae are moving between Cuban and American reefs,” said Jake Kritzer, an ocean and fisheries expert at the Environmental Defence Fund who participated in the expedition. “Not just groupers, not just snapper, but parrot fish, damsel fish, corals, shrimps, all the little invertebrates and all the fishes that live on a reef.”

“What it means is that what we do in terms of fisheries management of Cuban reefs can have effects on the abundance of different populations on US reefs, and vice versa,” he said.

A school of blue stripe grunts swim under elk Horn coral in a shallow reef in the Jardines de la Reina, a protected area in Cuba July 14, 2015. — Picture by Todd Heisler/The New York Times

On a recent morning in late May, the crew loaded up the Itajara with supplies for the day’s work: heavy fishing lines, hooks and bait, diving gear, coffee, water and beer.

The boat was docked at the research station in the mangroves off Anclitas cay, a no-frills wooden structure built atop a platform anchored by pilings. With its narrow walkways, the station seemed as much in the water as over it. Tarpon darted under the back deck. A school of sergeant major fish cruised by. A female crocodile, a longtime resident, rested motionless under a mangrove tree.

Today, the targets were bigger fish, like the goliath grouper, which can weigh up to 1,000 pounds — “like a small car,” Pina said — and of course, the sharks: Caribbean reef sharks, silky sharks, lemon sharks and other species that frequent the waters surrounding the coral reef here.

Visitors to Jardines de la Reina are impressed by the sharks, how many there are and how close they come to divers, circling them, coasting by them, gliding up for a look-see.

Already, during a snorkelling session at Pippin, two miles southwest of the research station, the members of the expedition had found themselves surrounded by silkies, their bodies pale white against the dark blue of the water. But the snorkelers, hands tucked into their bodies and feet covered by flippers, looked nothing like prey, and the silkies moved on.

The sharks are a tourist attraction — at two of the many diving spots in the Gardens, they are fed to ensure larger numbers — but to scientists like Pina and Kritzer, their very presence here is an indicator of the coral reef’s robustness.

A crocodile floats under a mangrove near a research station in the Jardines de la Reina, a protected area in Cuba July 14, 2015. — Picture by Todd Heisler/The New York Times

Research has linked the health of reefs to habitation by large fish, and the absence of sharks and other top predators is often a sign of a reef in decline.

“If you like coral reefs, you have to like sharks,” said David E Guggenheim, a marine scientist who has worked extensively in Cuba and runs trips to Jardines de la Reina through his organisation, Ocean Doctor. “They are critically important to maintaining population balance. If they’re gone, the algae can overgrow the reef and smother it.”

The resilience of this coral reef seems beyond question. The waters inside the preserve hold 10 times as many sharks as outside, Pina said, and goliath grouper, rare in many places, are often seen here.

Remoteness, several scientists said, probably accounts for some of the reef’s strength. Genetics may also play a role. But the reef here was not always as healthy; it has substantially recovered and thrived since the marine preserve, one of the largest in the Caribbean, was established nearly 20 years ago.

A study by Pina and his colleagues found that fish populations increased an average of 30 per cent since the sanctuary was created.

Yet the preserve alone cannot ensure the protection of sharks and other large predators, species that travel long distances and are unlikely to respect the boundaries of sanctuaries. Although fishing is banned in the smaller marine preserve, it is still allowed in the larger protected marine area that Cuba has designated a national park.

A puffer fish that was caught in a net during an otter trawl, which collects fish population data in specific areas, in the Jardines de la Reina, a protected area in Cuba July 14, 2015. — Picture by Todd Heisler/The New York Times

Rachel Graham, a whale shark expert and executive director of Maralliance, a conservation organisation, said that sharks were still actively fished in the national park, just outside the borders of the sanctuary. “There’s a lot of dipping into the edges,” said Graham, who has worked in Jardines de la Reina.

And further out, in the Gulf of Ana Maria, “All bets are off,” she said.

Regular surveys of the size, number and location of sharks in a given area provide information that can eventually help forge new strategies to reduce such fishing — Cuba is in the process of developing a national shark plan.

As long as the sharks and other large fish remain in Jardines de la Reina, the tourists will come, too, many of them staying at the Tortuga, a small floating hotel near the research station operated by Avalon, an Italian company, under a contract with the government.

Tourism is important to the marine preserve, for Cuba’s economy — it is ranked among the 50 top diving spots in the world and 60 per cent of divers cite sharks as the main attraction, Pina said — and as an incentive to keep the fishing ban in place.

The goliath groupers are also a big draw.

“Everybody likes big animals,” Pina said, “and the goliath grouper is like an elephant in the water.”

A Caribbean reef shark is held down in a boat while researches tag and release it in the Jardines de la Reina, a protected area in Cuba July 14, 2015. — Picture by Todd Heisler/The New York Times

Figueredo, an environmental economist, has devoted much of her work to calculating the monetary value of tourists’ diving with sharks, watching jacks and angelfish dart in and out of stands of living Elkhorn coral and fly-fishing in waters filled with tarpon and bone fish. Her studies, she hopes, will help Cuban officials develop guidelines for tourism in the smaller preserve and in the larger national park.

Tourism in large doses poses its own threat, however. Last year, under the government’s limits, fewer than 3,000 divers and fly-fishermen visited Jardines de la Reina. But the opening of relations between Cuba and the United States means that many more tourists may soon come.

Andrés Jiménez Castillo, a marine biologist who works as a manager at the Tortuga, said that many people were concerned about what will happen.

“We will have a lot of sailing boats and other kinds of boats that will be able to come here,” he said. “And we need to be ready.” — The New York Times