The study showed the genetic structure of nine Schrenk spruce stands, which represented altitude and geographical variants in the Tien−Shan mountains in Kyrgyzstan. Comparison between genetic structure of stands was based on frequencies of nuclear microsatellite (SSR) alleles occurring in three DNA loci. The total genetic differentiation of Schrenk spruce populations was low (FST=0.0651). Eight main groups of populations were distinguished in the dendrogram defined by Nei's genetic distances based on micro− satellite markers.