Recent changes in sylvicultural practices in Central Europe have created forests with closed canopies, and tree species preferring open and sunny forests have declined in area and abundance. This led to increased isolation of populations of many rare insect-pollinated, fleshy-fruited species with a naturally scattered distribution. To gain insight into the regional population dynamics of such species, we investigated the consequences of spatial isolation, population size and density on the genetic structure of Sorbus torminalis and simultaneously considered the relationship between fecundity and habitat quality. Genotype data for biparentally (ISSRs) and maternally inherited (cpDNA PCR-RFLPs) molecular markers were generated for 26 Swiss populations of S. torminalis. We applied analyses of molecular variance (amova) to both marker types and separated the relative contributions of pollen and seed dispersal to historical gene flow. amova detected significant differentiation among populations (ΦST ISSR = 0.107; ΦST cpDNA = 0.370) in both marker types. The relative rate of pollen to seed gene flow was low (r = 2.919) and significantly different from equality. Isolation by distance was weak within Eastern and Western Switzerland, although populations were substantially differentiated. Within-population molecular variance was not explained by population size, whereas habitat quality (openness) positively influenced the percentage of fruiting trees and the degree of fruiting per tree, indicating that more open forests enhance sexual reproduction. Our findings of significant genetic differentiation in the absence of clear geographical structuring can be explained by the distinct ecology of S. torminalis and nondirectional colonization events in metapopulation-like dynamics.