The allozyme analysis of six local populations of Pinus mugo Turra and six populations of P. sylvestris L. in the Ukrainian Carpathians, Swiss Alps, and Schwarzwald has shown a higher polymorphism and greater interpopulation differentiation of the Carpathian group of P. mugo populations compared to the Alpine group (Nei’s genetic distance DN ₇₈ at the level of geographic population group is −0.023). A genetic differentiation of DN ₇₈ = 0.049 between these populations, which are isolated by a distance of more than 1000 km, has been found. This confirms the existence of the subspecies P. mugo ssp. mugo and P. mugo ssp. uncinata in the Carpathians and Alps, respectively. The hypothesis is put forward that the former subspecies has been formed in the Balkans and the latter, in the Pyreneans. It has been demonstrated that regional populations and geographic groups of P. sylvestris are less differentiated than those of P. mugo.