Using a pair of primers selected for the loci deltau 215, deltau 281, and deltau 323 of Darevskia unisexualis monolocus PCR analysis of orthologous loci was carried out in populations of the related parthenogenetic species D. armeniaca and in populations of bisexual parental species D. valentini and D. mixta. It was shown that the studied loci were polymorphic and represented in populations of D. armeniaca by several allelic variants. We cloned and sequenced PCR amplification products of the allelic variants of deltau 215, deltau 281, and deltau 323 loci. It was found that allelic differences of microsatellite loci were caused by variation in a number of tandem repeats in the microsatellite clusters and point mutations in the flanking regions. Interspecies comparison of the orthologous locus deltau 215 between parthenogenetic species D. armeniaca and parental species showed that two allelic variants of deltau 215 in D. armeniaca were inherited from the parental bisexual species D. mixta and D. valentini. The third allelic variant was not found in parental species and appeared because of mutation processes in genome of parthenospecies. For the first time, the information about the molecular nature of allelic polymorphism of these microsatellite loci of parthenogenetic species D. armeniaca was received in this study.