The prevalence and occurrence of endophyte fungi in association of the plants growing in different regions of Kyrgyzstan have been investigated. It is established, that endophyte fungi were associated frequently with plants from families Chenopodiaceae, Rosaceae and Fabaceae. Genus and species diversity of endophyte fungi were identified. The species of endophyte fungi from family of Curvularia,Acremonium, Alternaria, Penicillium, Fusarium, Stemphylium and Cladosporium were dominated in the bodies of plants, growing in different regions of Kyrgyzstan