The only autochthonous population of Tatra chamois (Rupicapra rupicapra tatrica) occurs in the Tatra Mountains (northern Slovakia and southern Poland). Another population has been introduced to the Low Tatra Mts., while Alpine chamois (R. r. rupicapra) has been introduced to the neighbouring mountain ranges, Vel'ká Fatra and Slovenský raj. All these populations have undergone intensive bottlenecks. Any resulting low genetic variability would mean that only few genetic markers could be used for population genetic studies due to prevailing monomorphism. We tested 65 markers previously used in chamois or other Caprinae species, from which 20 most suitable loci for noninvasive genetic study of the Tatra chamois were selected. These polymorphic loci were used for optimisation of three multiplex sets and revealed a mean number of alleles of 2.1 and mean expected heterozygosity of 0.331 for the Tatra population. Low genetic diversity was also observed in the Low Tatra population while slightly higher values were obtained for Alpine chamois population in Slovenský raj. We subsequently assessed the amplification success rate for noninvasively obtained samples (faeces), which ranged from 85.1% to 92.7% for particular loci. The developed polymorphic microsatellite sets provide a unique tool for population genetic study of the endangered Tatra chamois, even when using noninvasive sampling, and is also suitable for Alpine chamois.