Background <p>The parti-coloured bat (<i>Vespertilio murinus</i>) is a widely distributed species across Eurasia, notable for its facultative, seasonally occurring male-only colonies, which are uncommon in the bat world. Males benefit from social warming and social foraging during spermatogenesis. However, little is known about the relatedness between individuals within these groups. Our aim was to create a panel of microsatellite <i>loci</i> for use in genetic studies of parti-coloured bats, as understanding the evolutionary mechanisms leading to male sociality cannot be done without using genetic techniques.</p> Findings <p>Of 27 microsatellite <i>loci</i> that had previously been used for other species of the Vespertilionidae family, we selected 12 that provided reliable quality results with <i>Vespertilio murinus</i> samples. The number of alleles at each <i>locus</i> ranged from 3 to 40, and observed heterozygosity ranged from 0.002 to 0.589. Almost all markers showed a departure from Hardy-Weinberg equilibrium and presence of null alleles.</p> Conclusion <p>The presented microsatellite panel will be a valuable tool for studying the genetic relatedness of male colonies of parti-coloured bats.</p>