Jardines de la Reina, a vibrant marine preserve, is thriving even as other ocean habitats decline.

HAVANA, 15 Julio  JARDINES DE LA REINA,  (By ERICA GOODE)  The six-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?” Dr. Pina’s wife, Tamara Figueredo Martín, asked.

“Excellent, the condition is excellent,” Dr. 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 Center for Coastal Ecosystem Research, Dr. 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 colored 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, Dr. 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 Dr. Pina’s center played a role in the government’s decision to designate a marine protected area of about 830 square miles in 2010.

But Dr. 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.

Scientists like Dr. Pina have only just begun to explore and document the wealth of aquatic life in the waters of the archipelago and the Gulf of Ana Maria to its north: how many species there are, the size of their populations, how they move from one area to another and where their spawning and nursery grounds are.

But such knowledge is essential, scientists say, not only to manage the marine preserve effectively but also to develop conservation strategies for fisheries in a country where overfishing has taken a significant toll. What scientists learn from studying Jardines de la Reina may also help rescue and protect reefs in other regions where they are faring far less well.

An otter trawl pulled up an assortment of sea creatures, including a West Indian sea egg, a blue-striped grunt, a cushion sea star and a spotted trunkfish. Credit Todd Heisler/The New York Times

Dr. Pina has been fortunate, receiving some financing and equipment from American foundations, like the Pew Charitable Trust, which gave him a marine fellowship in 2012, and environmental organizations like the Environmental Defense Fund, which organized a recent expedition here for a group of scientists from the United States. Three New York Times journalists accompanied the group.

But 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,” Dr. Pina said.

Like other researchers, he hopes that the recent warming of relationsbetween 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 Center for Marine Research who is also doing work in Jardines de la Reina and has collaborated with Dr. 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 Defense 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 U.S. reefs, and vice versa,” he said.

With its abundance of fish and lush seagrass beds, Jardines de la Reina has been called the Galapagos of the Caribbean. Credit 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.

The previous day’s task had been to survey fish in the Caballones Channel, west of the archipelago, using an otter trawl, a large net with two wooden “doors” to keep it open.

It was only the second time that Dr. Pina had tried the trawl here — the research tool was acquired only recently — and he hoped it would be useful in evaluating the channel’s role as a nursery for fish, comparing the catch with samples taken in other locations. Knowing which areas are important as spawning and nursery grounds, marine scientists say, can help in developing more effective ways to protect them.

As he called out instructions to the crew, they dropped the trawl from the stern, left it in the water for two minutes as the Itajara slowly pulled it along, then drew it back in.

Hutias, nutria-like rodents, are hunted and eaten in some parts of Cuba. But in the safety of the marine preserve, they are happy to share a bottle of water. Credit Todd Heisler/The New York Times

After seven trials, the catch was interesting but modest. It included two slender filefish (Monacanthus tuckeri), a bulging-eyed Webb Burr puffer (Chilomycterus antillarum), a sea star and a 5.6-ounce spotted trunkfish (Lactophrys bicaudalis).

“If you did this enough, you’d see some really big trawls and some with nothing,” Dr. Kritzer said, “which means you have to do a fairly big number of samples to get a pattern out of that noise.”

Yet the yield was small enough that Dr. Pina wrote in a later report that other areas seemed to provide better nurseries for juvenile fish.

Today, the targets were bigger fish, like the goliath grouper, which can weigh up to 1,000 pounds — “like a small car,” Dr. 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 snorkeling 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 Dr. Pina and Dr. Kritzer, their very presence here is an indicator of the coral reef’s robustness.

A Caribbean reef shark cruises through the water in Jardines de la Reina. There are 10 times as many sharks inside the marine preserve here as in the waters outside. Credit 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 organization, 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, Dr. 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 Dr. Pina and his colleagues found that fish populations increased an average of 30 percent 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.

Rachel Graham, a whale shark expert and executive director ofMaralliance, a conservation organization, 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 Dr. Graham, who has worked in Jardines de la Reina.

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

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 Dr. Pina and his colleagues found that fish populations increased an average of 30 percent 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.

Rachel Graham, a whale shark expert and executive director ofMaralliance, a conservation organization, 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 Dr. Graham, who has worked in Jardines de la Reina.

A Caribbean reef shark pulled up on a long line, tagged and released will help Fabián Pina Amargós and his colleagues learn more about their biology and travel patterns. Credit Todd Heisler/The New York Times

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.

So in the late morning, the Itajara headed south to Las Auras channel, where the coral reef drops off into 80-foot-deep water, on a search for the large aquatic predators.

Once in the channel, 50 circle hooks were attached to a long fishing line, each separated by about 30 inches. The hooks, Dr. Pina said, are designed to protect the fish, staying in the mouth rather than moving into the stomach, where they can cause significant injury.

The big reef shark came up with the first hook, followed by two others under three feet long and less than six months old.

The variance in age and size was a good sign, Dr. Pina said, indicating that the channel was providing a home not only for adult sharks but for immature fish as well.

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 theTortuga, 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 percent of divers cite sharks as the main attraction, Dr. Pina said — and as an incentive to keep the fishing ban in place.

The goliath groupers are also a big draw.

The research station in the mangroves off Anclitas cay feels as if it is almost a part of the water. Tarpon and barracudas swim beneath the porch. A crocodile is a longtime resident. Credit Todd Heisler/The New York Times

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

Ms. 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.”

He is hoping, he said, that the diving and fly-fishing quotas will remain intact and the government will increase prices instead, keeping the area exclusive.

But Cuba’s capacity for enforcement is limited, and a coral reef is a sensitive ecosystem, easily damaged by hastily dropped boat anchors or careless divers.

And if 100,000 or even a million visitors were to descend on the marine preserve, Dr. Pina said, “The footprint on nature would be large.”