Isolated and island-like populations at the periphery of a geographic range of a given species are usually predicted to have low genetic diversity due to founder effect, habitat fragmentation, and bottleneck and/or inbreeding. As for parasitic plants, they may be more vulnerable to environmental and demographic stochasticities, habitat degradation, and genetic limitation because of their specialized life-history strategies depending on i.e. host plants. Pedicularis sceptrum-carolinum is a hemiparasitic species with a strongly fragmented geographic range in Eurasia whose small, isolated, island-like populations are scattered at the periphery of its geographic range. I studied its genetic diversity patterns at the western periphery of the species' range (Poland) using AFLP markers in order to unravel how isolation, population size and life-history traits (i.e. type of reproduction) influence its population genetic structure. Despite the geographic isolation among the four investigated populations (ca. 35–350 km), and irrespective of their small population sizes (14–50 individuals) and areas (6–100 m2) they preserved relatively high genetic diversity (Fragpoly= 46.7%-54.6%, Shannon's I = 0.222-0.241) in comparison with other polyploid, long-lived and outcrossing perennials, and significantly higher than that in the other Pedicularis species. Among the factors generating such high genetic diversity is the polyploid origin of this species. Additionally, sexual reproduction, the breeding system, and seed dispersal seem responsible for the patterns of within-population spatial genetic structure. The moderate genetic differentiation among populations (FST = 0.154) and the evidence of recent genetic admixture of populations, as well as genetic similarity among all investigated individuals suggested that gene flow may be relatively high and multi-directional, reflecting recent range expansion of the study species in Europe. I considered that the estimates of genetic differentiation supported the possibility of repeated colonization from different source populations.