Aim Our aims were to test whether morphological species of mountain pines were genetically supported in the western part of the distribution range of the Pinus mugo species complex (Pinus mugo Turra sensu lato), to resolve genetically homogeneous clusters of populations, to determine historical demographic processes, and to assess the potential hybridization of mountain pines with Scots pine, Pinus sylvestris L.Location Populations were sampled in the Iberian System, the Pyrenees, the French Mont Ventoux, Vosges and Jura mountains, the Germán Black Forest and throughout the Alps. This corresponded to a range-wide sampling for mountain pine sensu stricto (Pinus uncinata Ram.) and to a sampling of the western parts of the ranges of dwarf mountain pine (Pinus mugo Turra sensu stricto) and bog pine/peatbog pine [Pinus rotundata Lmk/Pinus X pseudopumilio (Willk.) Beck].Methods In total, 786 individuáis of P. mugo sensu lato from 29 natural populations, and 85 individuáis of P. sylvestris from four natural populations were genotyped at three chloroplast microsatellites (cpSSRs). Populations were characterized for standard genetic diversity statistics and signs of demographic expansión. Genetic structure was explored using analysis of molecular variance, differentiation statistics and Bayesian analysis of population structure (BAPS).ResuIts One hundred haplotypes were identified in P. mugo sensu lato. There was a strongerdifferentiationbetweengeographicalregionsthanbetweenmorphologically identified taxa (P. mugo sensu stricto, P. uncinata and P. rotundata/P. X pseudopumilio). Overall genetic differentiation was weak (G S T = 0.070) and displayed a clear phylogeographic structure [N S r = 0.263, N S r > N S r (permuted), P < 0.001 ]. BAPS identified a Pyrenean and an Alpine gene pool, along with several smaller genetic clusters corresponding to peripheral populations. Main conclusionsThe core regions of the Pyrenees and Alps were probably recolonized, respectivelybyP. uncinata and P. uncinatalP. mugo sensu stricto, from múltiple glacial refugia that were well connected by pollen flow within the mountain chains. Pinus rotundata/P. X pseudopumilio populations from the Black Forest, Vosges and Jura mountains were probably recolonized from various glacial populations that kept their genetic distinctiveness despite late glacial and early Holocene expansión. Marginal P. uncinata populations from the Iberian System are compatible with elevational shifts and long-term isolation. The causes of haplotype sharing between P. mugo sensu lato and P. sylvestris require further research.