During these years FUNZEL ran a program for the compliance of the accords on the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) in El Salvador, funded by the PROARCA-CAPAS/USAID project, oriented to decision-making levels: Legislative Assembly, Agricultural Quarantine, Environmental Police, Ministries, among others, to make them aware of the commitment to this international instrument signed by 183 countries, worldwide.

FUNZEL creates the first Wildlife Rescue and Rehabilitation Center, in support of the CITES Administrative Authority and later in alliance and support to the Ministry of Environment and Natural Resources- MARN. With this alliance, large seizures, from Nicaragua and Honduras, mainly of parakeets, parrots, green and black iguanas. The Center was closed after the 2001 earthquakes.

A research study by FUNZEL identified the Gulf of Fonseca and the Bay of Jiquilisco as the main sites in the entire Eastern Pacific Ocean where the hawksbill turtle, a species declared critically endangered worldwide, nests and forages. This work was the prelude for the environmental authorities to promulgate, in 2009, the Decree of prohibition to the consumption of eggs of sea turtles and their parts, taking FUNZEL the leadership in the conservation programs accompanying the Decree.

With financial support from alliances with the private sector and banks, FUNZEL has kept managing six nesting sites. It has an Environmental Education Program, offers conservation talks, training to the private sector and the "Clean Beaches" program. Maintains a permanent campaign through the media, social networks, television and radio.