Population genetic analysis becomes more and more popular as a tool to use in animal conservation (Broquet, Petit, 2009). The common or hazel dormouse (<i>Muscardinus avellanarius</i>) is a member of the rodent family <i>Gliridae</i> (Juškaitis, 2008a). These rodents are vulnerable to natural habitat changes, and because of this monitoring of the common dormouse was carried out in many countries (Bright et al., 2006), but there is still lack of genetic data. It is well known that microsatellites are being used to investigate the genetic structure of natural populations (Balloux, Lugon-Moulin, 2002). In our study we used 5 microsatellite primers to investigate 17 common dormouse samples from different places in Lithuania and Latvia. For DNA extraction non-invasive hair samples were used. The results show that the Mav023 primer with 13 alleles is the most informative primer, while the Mav002 primer with 2 alleles is the least informative one. The expected heterozygosity (He) per locus was between 0.5 and 0.743, and the observed heterozygosity (Ho) per locus was between 0.463 and 1, except Mav005 with 0.257.