The greatest variety of fish in Honduras is undoubtedly found in the reefs and surrounding waters of the Bay Islands, which contain an estimated 96 percent of all the marine life found in the Caribbean. Fish of all sizes, from tiny chromides to the whale shark, the world’s largest fish, are found near the islands.

A list of smaller fish species in the Caribbean waters off Honduras, with all the distinct species living on the reef, in deeper water, and along the coast, would go on for pages. A few of the colorful favorites on the reef include grouper, butterfly fish, barracuda, yellowtail snapper, Goliath fish, and angelfish. Other marine animals often seen on the reef are eagle and manta rays, green moray eels, sea horses, octopi, and sea turtles, to name just a few of the more prominent residents.

In their 100–150-year life span, whale sharks can grow up to 15 meters long, with a weight of nearly 12 tons. Daunting though they may be, whale sharks are harmless to humans, living off plankton and tiny shrimp, which they filter through their gill rakers as they cruise the deep waters north of the Bay Islands. The blunt-snouted, speckled fish are equipped with two sets of dorsal fins toward the tail and a pair of larger pectoral fins. The Bay Islands region is one of the few places in the world where whale sharks can be seen all year, most commonly in the waters near Utila, particularly February–April and August–September. Utila’s population is made up of whale sharks roughly 6–10 meters in length, and 15–20 tons in weight.

Other inhabitants of the deeper waters around the islands and off the north coast are wahoo, king and Spanish mackerel, bonito, blackfin tuna, kingfish, and marlin, while famed fighting fish such as snook and tarpon live in the lagoons along the coast, at the intersection of fresh and salt water.

Sharks, such as hammerhead, nurse, and blacktip, frequent the deeper waters along the Caribbean coast of Honduras. The waters of the Mosquitia are particularly notorious for hammerheads, and more than a couple of Miskito lobster divers have stories to tell about unpleasantly close encounters with these aggressive sharks. Don’t go swimming out beyond the waves in the Mosquitia! While sharks frequent the waters around the Bay Islands, there have been no reports of divers being attacked. A variety of other sharks live in the Pacific near Honduras, but they rarely make it into the Golfo de Fonseca. If they do, local fishermen promptly catch them and turn them into fillets.

Several species of shellfish are found in Honduran waters, particularly lobster, shrimp, conch, and a kind of crayfish found in the lagoons and swamps of the north coast. Lobster- and shrimp-fishing is a major industry on the north coast and in the Bay Islands, and shrimp-farming is also big business on the Golfo de Fonseca.

Resident freshwater fish include tilapia (found particularly in Lago de Yojoa), largemouth bass, catfish, mollies, minnows, and mojarras. Mountain trout and related native species, like guapote, tepemechin, and the endangered cuyamel, still live in Honduran rivers. This last fish, very meaty and tasty, once abounded in the rivers all along the north coast but has been fished to near extinction everywhere except a few places in the Mosquitia and Olancho.

The temperate waters surrounding the Bay Islands are an optimal habitat also for coral, of which some 73 types have been identified, along with 41 species of sponge. Staghorn and elkhorn corals, widely decimated in the Caribbean during the 1980s, are still relatively plentiful near Roatán. The reef forms part of the Mesoamerican Barrier Reef.