Highlights• Genetic diversity parameters and meiotic recombination frequencies in the relict populations were comparable to those from widespread localities.• Contribution of seeds without ovule was very high.• Fully developed seeds germinated better in central populations.• Significant differences of groundwater parameters were observed between relict and central populations. AbstractIn the present study, the impact of geographical isolation and habitat conditions on genetic diversity and sexual reproduction was tested in four relict populations of dwarf birch Betula nana L. in Poland and Belarus. Amplified fragment length polymorphism (AFLP) method revealed that the endangered central European stands were not genetically extirpated compared with the widespread localities from Finland and Russia, which can result from infrequent outcrossing events in long-living clonal populations. However, genetic clustering methods indicated significant differentiation of the Polish populations because of their small sizes and long-term geographical isolation. Considerable numbers of empty seeds were observed in both relict and central locations, although fully developed seeds germinated better in widespread populations. Analysis of groundwater chemical parameters indicated that two relict populations were significantly different from the remaining samples with respect to pH, electrical conductivity and concentrations of phosphorus ions, which can also influence the efficiency of sexual reproduction. In the light of results obtained it seems that endangered B. nana localities are relatively stable.