The Siberian jay Perisoreus infaustus is a bird inhabiting old-growth coniferous taiga forests. It has recently declined in numbers in Finland mainly because of habitat fragmentation. Distant mtDNA lineages from Taimyrian Peninsula (subspecies P. i. monjerensis) and middle Yenisei valley (P. i. rogosovi) have diverged from Fennoseandian (P. i. infaustus) lineage ca 610000 yr ago. The estimated time to the most recent common ancestor for Fennoscandian population (78000 yr) coincides with the beginning of the Weichselian ice age. Within Fennoscandia, the observed distribution of pairwise genetic distances followed the expected distribution of an expanding population reflecting the postglacial history rather than the present day situation of the Siberian jay. Mitochondrial control region sequences showed that among 65 Fennoseandian individuals the most common baplotype (40%) was found in all but two populations. Genetic structuring (φST= 0.111) was clear within the Fennoseandian population. This may be attributable to low intrinsic natal dispersal. In an isolate of western Finland, nucleotide diversity was significantly lower than in P. i. infaustus populations of the continuous distribution area. We suggest that isolation by habitat fragmentation in modern landscapes may effectively reduce gene flow below the level occurring in natural conditions. Thus, Siberian jay isolates with limited number of individuals would be highly vulnerable to loss of genetic variation or even to extinction by demographic or environmental stochasticity.