The stone crayfish, Austropotamobius torrentium, is one of the oldest freshwater crayfish species in Europe. Most Carpathian populations are in Romania, with a distribution clustered in 2 compact metapopulations in the western part of the country. Our goal was to understand if this pattern is the result of a coincidence or a complex set of restrictive circumstances. Romania is an ideal place to analyze crayfish distributions because they have not been disturbed by species translocations or massive loss of populations. We recorded the presence/absence of crayfish and measured 15 habitat variables at 428 randomly chosen headwater sampling sites, and analyzed the crayfish distribution pattern with a boosted regression tree model. Our results show that most of the Romanian territory is ecologically suited to support stone crayfish under current conditions. The most important influences on probability of presence were water velocity, conductivity, altitude, river size, and dissolved O₂. When included as a supplementary predictor in the model, the distance from karst became the strongest variable accounting for the probability of presence and explaining the current distribution of the stone crayfish. We propose the hypothesis that at least one cycle of Pleistocene glaciation shaped the current distribution pattern by causing massive extinction in the Carpathians, except in karstic underground water bodies that offered ecological refuges. After the glaciations, stone crayfish expanding from these refuges competed with colonizing noble crayfish Astacus astacus, restricting stone crayfish to insular areas.