Ask anyone to picture a coral reef and they almost certainly think of sun-dappled aquatic communities in clear, turquoise waters. While that is the norm for the majority of the world’s reefs, there are striking exceptions—one of which can be found in the muddy waters off northern Brazil’s coast, where the Amazon River meets the sea.

Researchers previously had a vague idea of the reef’s existence, but until now they had no inkling of just how large and diverse it truly is. The most extensive study to date, published today in Science Advances, reveals that the reef covers an area larger than Delaware—some 3,600-square miles, stretching from the French Guiana border to Brazil’s Maranhão State—and likely supports many species previously unknown to science. The reef is so odd, in fact, that its discoverers believe it may constitute an entirely new type of ecological community.

“This is something totally new and different from what is present in any other part of the globe,” says Fabiano Thompson, an oceanographer at the Universidade Federal do Rio de Janeiro in Brazil. “But until now, it’s been almost completely overlooked.”

The mouth of one of the world’s largest rivers is an unlikely place for a coral reef. The Amazon accounts for a whopping 20 percent of the world’s river-to-ocean discharge, and the tremendous muddy plume it produces in the Atlantic can be seen from space. “You wouldn’t expect to have gigantic reefs there, because the water is full of sediment and there’s nearly no light or oxygen,” Thompson says.

But in the 1950s, a U.S. ship collected a few sponges there, which suggested something bigger could be below. Another group in the 1977 found reef fish and sponges in an area near the mouth of the Amazon, as did a few scattered teams of researchers in the 1990s, including one headed by Rodrigo Moura, lead author of the new study and a marine biologist at the Universidade Federal do Rio de Janeiro. In 2015, interest began picking up: researchers from Brazil and Canada took samples at 79 sites in the reef's northern stretches and confirmed the presence of the 38 coral species there. This latest study expands on those results.

“Until now, only 0.001 percent of the total area was covered, because people had only sampled a few points,” Thompson says. That can probably be explained by how difficult the reef is to access: It is situated at depths ranging from 160 to over 320 feet, and the sea there is very rough.

In late 2012, Thompson and his team, mostly Brazilian researchers along with one American, began surveys of the reef system, conducting a second mission in 2014. They used sonar instruments to map the reefs, along with metal dredges and trawls to collect samples. While those destructive methods are not ideal, Thompson says they were necessary for collecting initial evidence of the reef’s presence and identifying the species that live there. In the future, remotely operated vehicles equipped with cameras and lights could be employed.

The researchers discovered that the reef sits at depths below the Amazon’s large plume of muddy fresh water. The pH, salinity and amount of sedimentation and light that characterize the habitat, though, are drastically different compared with what is found at other reefs around the world.

More species turned up in the sunnier central and southern waters than in the more sediment-rich northern ones, which are closer to the Amazon. But the Brazilian reef, overall, had lower biodiversity than the Great Barrier Reef and other traditional coral reefs, which host a quarter of all marine species.

One striking feature of the reef was its high densities of rhodoliths, a type of red algae that is often confused with coral because of its calcium carbonate structure and bright colors. These tennis ball-shaped organisms often covered the Brazilian reef floor. Sponges were the other major component of the reef system, with 61 species found. The team also counted 73 fish species, 35 algae, 26 soft corals, 12 stony corals and more.

Of the sponges, the team found 29 specimens that they have yet to identify and suspect constitute new species. They also uncovered unique microbes that seem to base their metabolism not on light but on minerals and chemicals such as ammonia, nitrogen and sulfur. Identifying and better understanding those species will require further taxonomic study, which is now underway. But the team believes there is enough evidence to recognize Brazil’s reef as a unique ecosystem. “The oceanographic conditions, unique metabolic features and the new biodiversity allow us to argue that this system is a new biome,” Thompson says.

Walter Goldberg, a coral biologist at Florida International University, who was not involved in the study, says the new research “greatly expands” what is known about Brazil’s reef system.

Carlos Daniel Perez, a marine biologist at the Universidade Federal de Pernambuco in Vitoria de Santo Antao in Brazil, who also was not involved in the work but was one of the authors of the 2015 paper, adds that the Brazilian reef may serve as a corridor for species that span the Caribbean and South Atlantic. Studies such as this one, he says, are critical for identifying those important areas and designing environmental management protocols to protect them.

Thompson and his colleagues agree that reef’s uniqueness warrants protection—especially in light of the fact that major oil and gas companies are exploring areas nearby for drilling. The researchers also point out that the reef probably plays an important role in sustaining fisheries that local communities depend on.

There is much left to be discovered. Though this study represents the largest survey ever conducted of the reef, it covered only about 10 percent of the entire system. “We have only rough map, not a very fine one,” Thompson says says. “We still have another [3,240-square miles] to describe.”

Editor's note, April 28, 2016: This article has been modified to clarify the extent of the 2015 study on the Brazilian reef.