BACKGROUND: Hybridization is a known phenomenon in nature but its genetic impact on populations of parental species remains less understood. We investigated the evolutionary consequences of the interspecific gene flow in several contact zones of closely related pine species. Using a set of genetic markers from both nuclear and organellar genomes, we analyzed four hybrid zones (384 individuals) and a large panel of reference allopatric populations of parental taxa (2104 individuals from 96 stands). RESULTS: We observed reduced genetic diversity in maternally transmitted mitochondrial genomes of pure pine species and hybrids from contact zones compared to reference allopatric populations. The distribution of mtDNA haplotypes followed geographic rather than species boundaries. Additionally, no new haplotypes emerged in the contact zones, instead these zones contained the most common local variants. However, species diverged significantly at nuclear genomes and populations in contact zones exhibited similar or higher genetic diversity compared to the reference stands. There were no signs of admixture in any allopatric population, while clear admixture was evident in the contact zones, indicating that hybridization has a geographically localized effect on the genetic variation of the analyzed pine species. CONCLUSIONS: Our results suggest that hybrid zones act as sinks rather than melting pots of genetic diversity. Hybridization influences sympatric populations but is confined to contact zones. The spectrum of parental species ancestry in hybrids reflects the old evolutionary history of the sympatric populations. These findings also imply that introgression may play a crucial role in the adaptation of hybrids to specific environments.