Phase I of CARPE began operating out of Washington, D.C in 1997 and centered on gathering information on the Central African forest ecosystem, while simultaneously building regional human resources and institutional capacity.

The program began in four countries; the Central African Republic, Equatorial Guinea, Gabon, and the Republic of Congo. Since its beginning five additional countries have been added; Burundi, Cameroon, the Democratic Republic of the Congo, Rwanda, and Sao Tome & Principe.

In 1997, there were no USAID missions in Congo Basin countries and the decision was made to work directly through partner organizations already operating in the region. The first set of ten partners included: the Wildlife Conservation Society (WCS); the World Resources Institute (WRI); World Wildlife Fund (WWF); World Learning (later succeeded by Innovative Resource Management (IRM)); the U.S. Forest Service (USFS); the Peace Corps; and the National Aeronautics and Space Administration (NASA)‚ in collaboration with the Universities of Virginia and Maryland. The tenth partner‚ the Biodiversity Support Program (BSP), a USAID-funded consortium of the World Wildlife Fund‚ The Nature Conservancy‚ and the World Resources Institute‚ handled program management until its Global Bureau cooperative agreement ended in December‚ 2001.

Four other partners began participating in CARPE in 2000: the World Conservation Union (IUCN); Conservation International (CI); the African Wildlife Foundation (AWF); and the U.S. Fish and Wildlife Service (USFWS).

In January of 2003, CARPE began its second strategic phase and officially transferred management to the region. CARPE Phase II is being operated as a regional Strategic Objective (SO) managed through the environmental sector of USAID in the Democratic Republic of the Congo (DRC). Phase II is projected to continue until September 11, 2011 and is specifically concerned with supporting sustainable natural resource management in the field, improving environmental governance, and strengthening natural resource monitoring capacity in Central Africa.

The implementation of Phase II corresponded with the launching of the Congo Basin Forest Partnership (CBFP) at the 2002 World Summit on Sustainable Development. At the summit, the U.S. Government (USG) committed $53 million to finance the CBFP's efforts to support sustainable forestry, biodiversity conservation, and poverty alleviation. The USG identified CARPE as the principal mechanism through which these funds would be dispersed.

From 2003-2005 USAID-CARPE dispersed approximately $15 million per year to promote the objectives of the CBFP and the following Administrative and Legislative Priorities: the Congo Basin Forest Partnership Presidential Initiative, the Global Development Alliance, the Presidential Initiative Against Illegal Logging, the Global Climate Change Initiative, the Biodiversity Legislative "earmark" FAA Section 118, the Tropical Forestry Legislative "earmark" FAA Section 119, and the Microenterprise "earmark".

At its current level of funding, CARPE represents the United States' largest conservation project in Africa. CARPE has requested a similar level of funding through 2007 and it continues to serve as the USG primary means of contribution to the CBFP.

In addition to the funds provided through the USG, CARPE requires matching funds from its primary partners amounting in aggregate to more than 50% of USAID's contribution. Thus far, the primary partners serving as executing agencies have been successful at leveraging approximately $150 million in support from international donors and non-USG sources.

At the completion of Phase II in 2011, a third CARPE strategic phase is expected to continue through 2016. Phase III is projected as the final period of transfer, when CARPE activities will be turned over to Central African institutions.