WCS in Honduras and Nicaragua is primarily active in one of the five largest forests in Mesoamerica known as La Moskitia or the heart of the Mesoamerican Biological Corridor. La Moskitia forest is a region that crosses Honduras and Nicaragua and has a great biodiversity of flora and fauna. The existence of La Moskitia is very important to ensure the genetic richness of the Mesoamerican tropical forests.
La Moskitia encompasses the largest reserves of the National System of Protected Areas of Honduras (SINAPH), these are:
- Hombre y Rio Plátano Biosphere Reserve.
- Tawahka-Asangni Biosphere Reserve.
- Warunta National Park.
- Patuca National Park
In Nicaragua, the protected areas of the National System of Protected Areas (SINAP), located within the region are:
- Bosawas Biosphere Reserve.
- Cerro Saslaya National Park
- Cayos Perlas Wildlife Refuge.
WCS has begun to carry out activities on the northern coast of Honduras with the main objective of contributing to the conservation of the country's marine and coastal resources.