Allozyme data were used to assess the genetic structure between 37 sympatric populations of the species-pair Silene vulgaris and S. uniflora ssp. petraea, and to infer levels of intra— and interspecific gene flow in the two species. Silene vulgaris is a geographically widespread weed of disturbed habitats whereas S. uniflora ssp. petraea is endemic to the Baltic islands of Öland and Gotland. On Öland, Silene vulgaris forms extensive linear populations along roads while S. uniflora ssp. petraea occurs in sparse and spatially-separated populations in open limestone habitats. Despite the differences in population size and structure between the two species, both species show extremely low levels of between-population differentiation. Between-site differences account for <2% of the total allozyme diversity within Öland in S. vulgaris, and <1% in S. uniflora ssp. petraea. Indirect estimates of gene flow are high for both species (Nm = 11 and 27, respectively). There is no relationship between genetic distance and geographic distance within either species, and the lack of genetic structure is consistent with the pollination biology of the species — both of which are predominantly moth-pollinated. The two species hybridize in intermediate habitats, and the geographic distribution of species-characteristic alleles indicates a potential for spatially extensive interspecific gene flow. Nevertheless, there are significant differences in allele frequencies between the two species and multivariate analyses show no overlap between populations of the two species. The species are ecologically separated by their different habitat preferences and by differences in their flowering phenology. There is no evidence that the endemic S. uniflora ssp. petraea is threatened by genetic contamination or assimilation by the widespread weed, S. vulgaris.