Hybridization is a widespread evolutionary process and a key source of evolutionary novelty. However, despite intensive study, the extent to which hybridization is deterministic and repeatable—particularly in recurrent contact events involving the same species under varying ecological conditions—remains unclear. Here, we investigated three replicated contact zones between Scots pine (Pinus sylvestris) and dwarf mountain pine (Pinus mugo) in Central Europe: two occurring in analogous peatland habitats and one in a contrasting sandstone outcrop. Using genome-wide SNP genotyping of over 1,300 individuals, we analyzed genomic structure, diversity, and ancestry patterns across these zones. All sites revealed pervasive hybridization, dominated by later-generation hybrids and a notable scarcity of pure P. mugo. Across environments, hybrid populations exhibited strikingly consistent genomic compositions, with asymmetric introgression strongly biased toward P. mugo ancestry—suggesting that hybrid genome structure may follow predictable patterns under similar ecological conditions. Nonetheless, we also detected site-specific differences in hybrid diversity and phenotype, highlighting the influence of local environmental selection on shared hybrid genomic backgrounds. We provide genomic evidence that Pinus uliginosa—a morphologically distinct peat bog pine traditionally regarded as a relic and endangered species—is instead an incipient hybrid taxon. Its genome reflects partial stabilization through hybridization and ecological filtering, yet it lacks sufficient genetic divergence to be recognized as a distinct species. Together, these results provide evidence for the repeatability of hybridization processes, which result in the formation of phenotypes reflecting a species continuum subjected to strong environmental pressures. The findings support the simplification of taxonomic nomenclature within the Pinus mugo complex, informing adaptive conservation strategies and the genetic management of hybrid lineages.