Closely related Pinus species, mountain pine (Pinus mugo Turra) and Scots pine (Pinus sylvestris L.), belong to native woody species in the Tatra National Park (TPN, southern Poland). Their occurrence in close proximity can lead to the formation of natural hybrids known as Pinus × rhaetica, which is a woody, often polycormic form. Pinus×rhaetica is described in the TPN, but there has been a great deal of disagreement over its origin. The goal of the studies was to verify the taxonomic status of individuals identified as Pinus×rhaetica that grew in the eight stands together with P. mugo and P. sylvestris by SSAP (Sequence Specific Amplification Polymorphism) analysis of transposon insertional polymorphism. In total, 34 Pinus×rhaetica, 25 P. mugo and 27 P. sylvestris individuals were tested in addition to 20 individuals of P. uliginosa from ‘Torfowisko pod Węglińcem' and ‘Wielkie Torfowisko Batorowskie' as well as 25 individuals of P. uncinata from the Austrian Alps as the control groups. Four transposon sequences were employed: a DNA transposon from the CACTA family, Tpo and retrotransposons – two gypsy (Ogre, IFG7) and one copia like (Bare). All species belonging to the Pinus mugo complex are highly variable with 49−81% polymorphic loci and genetic diversity, HTequals 0.228−0.307 with the highest values in Pinus×rhaetica. Surprisingly, P. sylvestris proves to be the least variable species, likely because of a narrow gene pool in small, scattered stands in the Tatras. Very low Nei's genetic similarities between P. sylvestris and Pinus mugo complex, especially in comparison with P. uliginosa (I=0.548) and P. mugo (I=0.558) exclude unequivocally the possibility of spontaneous hybridization among these taxa. Thus, it undermines the hypothesis about hybrid origin of Pinus×rhaetica in the Tatras. It proves to be a morphological form of P. mugo as assessed from the Nei's coefficient, I=0.985 which is well within a range of conspecific populations. Finally, none of the studied individuals of Pinus×rhaetica are derived from seeds of Alpine P. uncinata.