La Moskitia supports a diverse and rich assemblage of neotropical life, including many mammals and birds, species that are endangered or reduced in other parts of Central America. Important indicator species such as the harpy eagle (Harpia harpyja), jaguar (Panthera onca) and jaguia (Tayassu pecari) demonstrate that this area is still very rich in biodiversity and in some parts of the area the fauna and flora remains intact.

The coastal strip of the Moskitia contains a labyrinth of lagoons, canals and mouths with large expanses of sandy beaches, marshes and mangrove areas. Inland the terrain is more rugged and the terrain is dominated by hills and, eventually, mountains. The mountainous lands with hills and rocky topography cover the headwaters and interfluves of the rivers.

In the marine area, Honduras is part of the second largest coral reef in the world, the Mesoamerican Reef, habitat of a large number of marine species, so its conservation is vital for the world.

Sea turtles have found in the Caribbean coast of Nicaragua an ideal place for nesting, arriving annually turtles of the species Loggerhead (Caretta caretta), Hawksbill (Eretmochelys imbricata), Green (Chelonya Midas) and Leatherback (Dermochelys coriacea). The nesting beaches in the Pearl Cays are especially important for the long-term survival of the Hawksbill Turtle (Eretmochelys imbricatta), with an average nesting rate of about 700 nests per year making this one of the most important nesting sites for this species in the entire Caribbean.

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