Natural hybrid zones provide a valuable tool to study introgressive hybridization, because they can contain a wide variety of genotypes that result from many generations of recombination. Here we used molecular markers and morphological variation to describe the structure of two natural hybrid zones between Silene latifolia and Silene dioica in the Swiss Alps. Populations in both hybrid zones consisted of few intermediate hybrids and were dominated by backcross hybrids. The latter were also found in the parental populations at the margins of the hybrid zones. Out of 209 amplified fragment length polymorphism (AFLP) markers scored in 390 individuals, only 7 (3.3%) were species specific. These results indicate that introgression between S. dioica and S. latifolia is extensive, and that hybrid zones act as bridges to gene flow between these two species. Analysis of linkage disequilibrium identified few populations in which hybridization is ongoing, whereas in most populations linkage disequilibrium has eroded. Where hybridization is ongoing, strong changes in species-specific marker frequencies and morphological traits were observed. Plastid introgression into the hybrid zone was found to be bidirectional, but only the S. latifolia plastid haplotype was found in a nuclear S. dioica background. This unidirectional plastid introgression from S. latifolia into S. dioica is most likely due to pollen-flow from S. dioica onto S. latifolia, and results in plastid capture. Comparisons between the molecular and the morphological hybrid indices revealed that morphology in this study system is useful for identifying hybrids, but not for detailed analysis of hybrid zone structure.