The genetic diversity and population structure of Arabidopsis thaliana on Valaam Island was investigated. The purpose of the study was to detect the molecular genetic mechanisms and microevolutionary processes in insulate populations of A. thaliana on an island lying in the northern periphery of the species range. The variability at 95 RAPD-loci was evaluated in A. thaliana from four localities on the island. A higher level of genetic diversity was revealed (average value P99 % = 29.2 %; Hexp=0.092) in comparison with other self-pollinators. The genetic variability of A. thaliana on Valaam was however lower than in previously investigated mainland populations of arabidopsis in Karelia. This fact is supposedly due to the island’s southerner location and milder climate, and may also depend on the low rate of gene migration from the mainland because of the species’ isolation on the island. The level of Nei’s genetic similarity of the studied groups of plants was high (average IN = 0.949). Nei’s gene diversity statistics showed that 39.0 % of the total gene diversity was explained by between-group variability (GST), which is quite low for inbred species. The findings allow to suggest that the species A. thaliana on Valaam is one but segregated population where subpopulations are connected to one another by migratory interactions. This population structure counteracts inbreeding, which happens in isolated populations of limited size, and contributes to the preservation of genetic diversity, which is essential for adaptation and survival of populations.