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The results of an analysis of microsatellite polymorphism in two closely related Arabidopsis species that differing by their crossing types are presented. Considerable genetic diversity was revealed in Arabidopsis thaliana populations located at the northern periphery of the species range (Karelia), which was not typical of self-pollinating species. Populations from the northern boundary of the species range in the basin of Lake Onega were found to be more polymorphic (P99% = 0.43; Hexp = 0.17) as compared to populations of the islands of Lake Ladoga, which are located approximately 300 km to the south (P99% = 0.39; Hexp = 0.15). It is suggested that the high population polymorphism of A. thaliana in the northern part of its range is most likely associated with hostile growing conditions and is the basis for the adaptation processes. A. thaliana populations are highly differentiated (G(ST) = 0.783), which is typical of inbred species. However, such a high interpopulation differentiation is probably due to the low level of gene flow. Specifically, five populations out of seven examined are located on the islands, i.e., are to some extent isolated. These great differences between A. thaliana populations in terms of polymorphism, as well as the high haplotype diversity, suggests postglacial colonization of the Karelian territory by many different ancestral forms. The participation of unique alleles of microsatellite loci with many dinucleotide repeats in the adaptive evolution of A. thaliana is discussed. A species population that is rare for Karelia, Arabidopsis lyrata ssp. petraea, is in complete isolation and, due to specific features of the microevolutionary processes in such populations, is characterized by the polymorphism level, which is low for outbred species (P99% = 0.64; Hexp = 0.16). Nevertheless, this population exists in Karelia for a long period of time, pointing to its successful adaptation to these conditions.