The mating system of small populations, isolated as a result of habitat fragmentation, is a key factor in their survival. As such populations are at risk of losing their genetic variation, reduction of their evolutionary potential is a distinct possibility. A flexible mating system may therefore provide a means of maintaining genetic variation. The mating system of the edible dormouse (Glis glis), a small arboreal rodent endangered by the fragmentation of its habitats, is not well understood. To date, only one study has provided evidence of multiple paternity in dormice. We present the results of a four‐year study of eight isolated dormouse populations. Using 138 individuals and 10 polymorphic autosomal microsatellite loci, we examined the prevalence of multiple paternity in these populations. In addition, we investigated the frequency of communal nesting and the genetic relationships between the females and juveniles occupying a single nest box. We found a high prevalence of multiple paternity (70% of the litters were multiple‐sired), a weak genetic relationship between the juveniles and the accompanying females (in 81% of cases the female residing with juveniles in a nest box was not their biological mother) and a 10.5% frequency of communal nesting in all nests. Given the low genetic variability of dormice, the multiple paternity and promiscuity observed in this species can help to maintain its genetic diversity.