This is the first study of the morphological and molecular variation in two peripheral populations of the butterfly Jutta Arctic, Oeneis jutta, a glacial relict species endangered by the fragmentation of its habitat in Poland. An analysis of the morphological characteristics indicates that both Polish populations are similar but differ significantly in some characteristics. Levels of genetic variation were assessed using mitochondrial cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 5 (ND5) gene fragments together with a segment of the mtDNA control region (CR) and a nuclear elongation factor-1a (EF-1a) gene sequence. In addition, the pattern of molecular variation in specimens from eastern and northern Europe was examined. Interestingly, the analysis of variation in a 932-bp sequence of the nuclear EF-1a gene in representatives of the populations studied revealed a relatively higher level of diversity than that of mitochondrial genes. There was evidence of divergence between the peripheral populations and lack of gene flow between them. The two closely situated populations had a high FST value (0.69), which clearly indicates their isolation. These populations appear to be demographically independent breeding units, with distinctive allele frequencies and consequently should be recognized as separate units for management and conservation. The preliminary results are in accord with an a priori subdivision based on collection areas and suggest that habitat fragmentation has affected the genetic diversity and structure of these populations.