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Batrachyla taeniata (Batrachylidae) is a small frog from Chile and Argentina with a distributional range that spans more than 1500 km. However, their populations are threatened due to the change in land use, deforestation, and human settlements. Through massive sequencing runs in ION Torrent PGM, was built DNA fragment library, from which we finally isolated and characterized 25 microsatellite loci from 40 individuals. The number of alleles per locus ranged from 2 to 23, allele sizes varied between 110 and 268 bp, observed heterozygosity ranged from 0.205 to 1.000 and the expected heterozygosity between 0.21 and 0.93. We found evidence of deviations of HWE for 10 microsatellite loci, linked to high inbreeding coefficients, indicating a loss of heterozygosity in those particular loci. There was no linkage disequilibrium found within the microsatellite loci tested through the sequential Bonferroni correction. These microsatellite markers can be used to evaluate population problems such as low diversity and high genetic structure, with the purpose of optimize future conservation strategies for the populations of this species.