Phylogenetic relations between four plant groups of apple tree Malus baccata (L.) Borkh, which grow in Rebublic of Buryatia, were studied using six highly polymorphic microsatellite loci. Groups were defined according to their geographic location. Higher degree of genetic isolation was found between groups of plants that were situated geographically close with each other. Thus, putative mechanism of the origin of dwarf forms of M. baccata can be the plants’ physiological adaptation to peculiar local environment conditions.