Honduras is Central America's second largest country, and boasts not only a mountainous landscape with dense montane and cloud forest, but also many Caribbean Islands. Despite these advantages the biodiversity of Honduras has been much less studied than other Central American countries such as Costa Rica, Panama and Belize.

In Honduras, the terrestrial research programme is run in conjunction with a Honduran NGO called ESAC (Expediciones y Servicios Ambientales de Cusuco). The purpose of this science programme is to provide data on socio-economics, forest structure and biodiversity (using indicator groups and population levels of key or threatened species) to assess the performance of the protected-area management. With the advent of funding mechanisms such as REDD (Reducing Emissions of greenhouse gases from Deforestation in Developing countries) these annual biodiversity surveys have taken on an even more important role. The purpose of the REDD funding is to provide a marginal cost advantage for governments and communities to protect their forests rather than allow deforestation, thereby protecting their carbon sequestration value and by implication their biodiversity value. However, since monitoring for the REDD scheme and release of payments is primarily based on regular analysis of satellite imagery to detect deforestation, in theory it is possible for a forest receiving REDD payments to be hunted out without the payments being affected. If this were to happen it would reduce the value of REDD and there would be little benefit to protecting natural forests over plantations - both would conserve carbon but the latter has little benefit in protecting biodiversity. Data sets such as those held on the Cusuco National Park where changes in the diversity of key taxa or population levels of key species can be tracked can be used to set additional biodiversity related criteria for receiving REDD payments. There are few forests in Honduras that have the level of biodiversity data that has been collected on the Cusuco Park which places Cusuco in prime position to receive such funding. The data collected to date on Cusuco have demonstrated that the Park contains 6 species of amphibian found only within the Park boundaries and a further 10 species of amphibian in the IUCN threatened category. In addition a new genus of tree (Hondurodendron) has recently been described from the Park.

The marine research programme is run in conjunction with the Honduran Coral Reef Foundation (HCRF) for the Cayos Cochinos sites and the Coral View Research Centre and Bay Island Conservation Association (BICA) on Utila and with Grupo de Apoyo al Desarrollar (GAD) on the northern Honduran coast. Surveys are being completed on the reefs around Rio Esteban on the mainland, reefs around Cayos Cochinos Islands which is a Marine Protected Area (MPA) but where there are no mangroves to act as fish nurseries, and reefs and mangroves around Utila.

The main research objective of this programme is to complete reef fish, coral and macro-invertebrate surveys using stereo video for the fish surveys and transect videoing for the benthic surveys on the reefs around Utila, the mainland adjacent to Rio Esteban and the Cayos Cochinos islands to provide annual monitoring data to inform the various organisations on the effectiveness of the current reef management. In addition,  the functioning of the mangroves on Utila as a fish nursery and in sediment stabilisation is being studied from mangroves that range from pristine to severely damaged. There are also unique reptile species found on Utila and the Cayos Cochinos Islands and long term ecological data sets are being gathered on these populations.