Dichoropetalum schottii is a species that lives at low to medium altitudes in the southern European mountain ranges, from the Balkans (N Greece) to the Pyrenees. Its legal protection status is not homogeneous along its distribution range, as only some of its edge populations, in the Pyrenees, are protected. Here, by means of allozyme electrophoresis, we examine the genetic variability of populations representing four different regions within its distribution area (Pyrenees, Maritime Alps, Karst Plateau in the SW Slovenia—NE Italy border region, and Pindus Mountains in Greece). The species as a whole exhibits relatively high levels of genetic diversity, partly due to the occurrence of several duplications among the loci surveyed. Genetic differentiation among populations and regions was low, which could be interpreted as the result of recent allopatric fragmentation. We conclude that the species as a whole is not threatened, and that the currently protected populations are, paradoxically, the least valuable from the genetic point of view.