Oligo- and mesotrophic wetlands, such as bogs, fens and swamps, have become more and more restricted in Europe, and wetland species related to them have increasingly been threatened. Due to increasing habitat fragmentation, the exchange of individuals of these species among sites and, as a consequence, gene flow has been reduced or even eliminated. Therefore, we analysed the genetic structure of 11 populations of an endangered stenotopic damselfly, Nehalennia speciosa (Odonata: Coenagrionidae), in Poland and Lithuania by means of allozyme electrophoresis of 14 gene loci. The overall genetic diversity of all populations was low (A: 1.32; H: 2.6%; Ptot: 29.2%), and no significant differences were observed among the different groupings of populations (degree of fragmentation, habitat type and size, population size). The genetic differentiation among populations was also low (FST: 2.0%) and no regional groups were detected. A low degree of isolation by distance was observed for genetic distances. Taking into account these results, the conservation effort for this species should be focused on large local populations and not necessarily on metapopulation structures. Furthermore, N. speciosa could be (re-)introduced in extinct patches and seemingly suitable localities. Genetically, such relocations should be feasible due to the generally high genetic homogeneity of populations.