Ecosystem Research and Implementation Center (EKOSAM) has undertaken a mission depends on "ecosystem-based" research. The concept of biodiversity includes genetics, species and ecosystem diversity. It is revealed that we need to protect not only the species but also genetic wealth and ecosystem processes. Preservation of diversity at the ecosystem level (for example, the protection of the food chain and energy flow) ensures the protection of all elements of biodiversity. Turkey has a very important place in the world in terms of ecosystem and species diversity since it takes place in the transition zone of Iran-Turan, Euro-Siberian and Mediterranean bio-geographies so that it has so many different climatic and topographical features. However, Turkey is one of the countries increasingly lost their natural habitat and its biodiversity is under threat. Both hosting high biodiversity, as well as being this biodiversity is under threat, Turkey is among the most important biodiversity hotspots in the world. Ecosystem-based research is necessary to examine natural resources and biodiversity management, which is very critical for our country, especially on the basis of aquatic, forest and steppe ecosystems and to lay the foundations of long-term monitoring infrastructure.