In this study, we analyze and compare the genetic structure of edible dormice representing five populations, inhabiting forest complexes in southwestern Poland that differ in their degree of fragmentation and isolation. Total genomic DNA was isolated from hairs with bulbs of 145 individuals captured between 2018 and 2020. All dormice sampled were genotyped at 14 microsatellite loci. Population genetic analyses showed that genetic variability in the studied dormice, assessed based on observed and expected heterozygosity as well as allelic richness, was on average very low (0.39, 0.43, and 2.83, respectively). In the populations studied, genetic structure was detected indicating two or five distinct genetic clusters, the existence of which can be attributed to either historical factors or modern human activity. Genetic differentiation between dormice living in the studied localities, determined by F_ST, ranged from 0.07 to 0.40 (all F_ST coefficients were significant at P < 0.05). A significant positive correlation was detected between genetic differentiation and geographic distance (r = 0.645, P < 0.017), indicating that genetic differentiation increases with distance, but no correlation between genetic differentiation and habitat barriers (r = 0.359, P < 0.132). The results of this research are compared to those of other European populations of edible dormice, and implications for the future of this endangered species are discussed.