Estimates of genetic differentiation at intra- and interspecific level are often hindered by the lack of suitable molecular markers. Low phylogeographic resolution limits development of appropriate conservation strategies especially in case of endangered forest tree species with small and disjunct distribution. In this study, we assessed fine-scale genetic structure of relict and endangered peat bog pine (Pinus uliginosa) and two other closely related European pine species (Pinus mugo and Pinus uncinata) using a set of 15 newly developed maternally inherited and seed-mediated mitochondrial DNA (mtDNA) markers and two previously known polymorphic mtDNA regions (nad1, nad7). Three main groups, corresponding in general to three investigated species were revealed in the haplotype network analysis. However, only P. uncinata was clearly distinct at all levels of analysis, whereas great genetic similarity and haplotype sharing was observed between P. uliginosa and P. mugo. Strong phylogeographic structure was found in P. uliginosa that showed high differentiation at relatively short geographical distance among populations and the existence of mitochondrial lineages of different evolutionary history. Hybridization with other pine species has likely contributed to genetic differentiation of P. uliginosa as indicated by contemporary distribution of mtDNA haplotypes. The research emphasizes the importance of accurate assessments of genetic structure of endangered species with complex evolutionary history for development of efficient conservation strategies.