Spotted suslik Spermophilus suslicus is one of the most endangered mammal species in Poland. Over the last 50 years, it lost more than 90% of its populations and about 70% of its individuals. In order to establish a conservation and reintroduction program, the knowledge of population structure of the species is crucial. We have developed nine polymorphic microsatellite loci to analyse the population structure. Six of the primer sets also amplify polymorphic markers in the European suslik Spermophilus citellus.