Distribution of cryptic species of green toads (Bufotes viridis and B. sitibundus) in Dagestan still understudied. We used the nuclear (microsatellite BM224) and mitochondrial (fragment of the CytB gene) markers characterized by species-specific alleles and haplotypes, respectively. Alleles of B. viridis predominated in toad populations in the plains in the north of the republic, while B. sitibundus alleles were more numerous in more southern mountainous and coastal (the coast of the Caspian Sea southeast of Makhachkala) regions.