The most valuable natural complexes and objects should be represented in the State protected areas (PA) system. In order to preserve biodiversity, it is necessary to expand protected lands to 10% of the total country area and create an ecological network that includes various categories of ecosystems. Each protected area can represent one or a number of ecosystems, depending on the height above sea level, landform, climate and other factors. In a perfect scenario, PA system of Kyrgyz Republic must represent all categories of ecosystems including mountain, steppe, semi-desert and desert. In this research the analysis of the representativeness of protected areas in Kyrgyz Republic was performed for the first time. For this purpose, GIS data sets for PAs and classification of ecosystems were used. According to the results, forest ecosystems have the highest coverage, whereas low mountain meadows and wetlands have the lowest coverage in PA system of Kyrgyz Republic. This research suggests that this type of analysis is an important tool for biodiversity conservation and evaluation of an ecological vulnerability.