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 newly formed Honduran NGO called ESAC (Expediciones y Servicios Ambientales de Cusuco). It is designed to produce comprehensive data on the biological value of the Cusuco montane/cloud forest National Park and to monitor change (both natural and human induced) in the communities of a wide range of taxonomic groups. The ultimate 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. 

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 Center and Bay Island Conservation Association (BICA) on Utila.  

The HCRF has published a management plan, which includes the declaration of a Marine Protected Area for the Cayos Cochinos islands (the CCMPA) and implementation of this plan is being supported by a range of NGO's (eg WWF, The Nature Conservancy, AVINA). The role of Operation Wallacea is to develop the research output from the main research centre on Cayo Menor and to provide data that can be used to assess the effectiveness of the management programme.  Declaration of the Marine Protected Area (MPA) has resulted in local communities living within and adjacent to the MPA losing fishing rights and therefore income. Opwall is working on the Northern Honduran coast to collect socio-economic data in order to establish how the incomes of the inhabitants of the regions affected by the existing management plan can be increased.  

Utila, in comparison with the Cayos Cochinos Islands, is developed for dive-based tourism, and the reefs therefore have an economic importance to the economy of the island, while being subjected to the many pressures that such an industry brings. This makes for an interesting comparison between the ecology of Cayos and that of Utila, and the factors affecting the ecology of both.