Human activity is perceived as the first reason for destruction of the environment. The expansion of the world population will therefore cause many environmental problems such as climate change, pollution of air and water, soil degradation, loss of ecosystems and biodiversity. Biodiversity is one of the largest environmental problems because its loss can have an irreversible effect. Invasive Alien Species is among the main threat to this biodiversity.The spread of those species in the world have been made ships by ballast water. Even if the Ballast water management convention adopted in 2004 is not yet enter into force; which create an obstacle to resolve the program. The GEF has developed a pilot project to help developing countries to deal with this project.With the result of this pilot project lot of developing countries can restructure their national legal and institutional framework in order to deal with this issue.In this paper after analyzing the GEF program activities in the protection of biodiversity; we demonstrate how this program is best way to deal with ballast water management issue in Cote d’Ivoire and what improvements the country must do for an effective implementation of the project.