Genetic variation was assessed in the endangered species C. variolosus (Coleoptera: Carabidae), which is listed in the European Habitats and Species Directive. Twelve populations from the north-western margin of its range in Germany and France to the border region between Slovenia and Croatia were investigated for variation at 16 allozyme loci. In general, genetic diversity was rather low as indicated by a mean allelic richness of 1.3 alleles per locus, a mean gene diversity (H E ) of 0.071 and a mean proportion of polymorphic loci (P 95% ) of 16%. Genetic diversity did not change directionally from the margin towards the core of the range. Very high differentiation between populations (overall F ST = 0.465), the results of a Mantel test, and poor accordance between geographical and genetic distance suggest a high degree of isolation of the island-like distributed populations. High F ST values and genetic distance measures, even between geographically close populations within the same drainage, confirm a very low dispersal power of this habitat specialist of headwater areas and swamps in woodlands, even in comparison with other flightless beetles. It is concluded that the majority of populations are demographically independent. Hierarchical F-statistics indicate that almost half of the genetic variance is found between regions and populations. Therefore, we recommend that conservation efforts consider every population as a management unit and aim to maintain as many populations as possible over as many regions as possible. © 2008 Springer Science+Business Media B.V.