<p>The Lear’s macaw (<i>Anodorhynchus leari</i>) is endemic to the biome of Caatinga, Brazil, and due to the small number of individuals remaining in the wild in a single population is classified as globally “Endangered” by the International Union for Conservation of Nature (IUCN). In addition to anthropogenic disturbances that cause habitat loss, one of the main threats to the species is international trafficking to feed the animal pet trade. This study aimed to evaluate the cross-species transferability and characterization of a new set of microsatellite loci identified in the genome of the scarlet macaw (<i>Ara macao</i>) to be applied in the <i>A. leari</i> genotyping, increasing significantly the number of microsatellite loci available for this species. Eighteen <i>A. macao</i> polymorphic microsatellite loci were selected to be tested here and were amplified successfully. Sixteen loci showed to be polymorphic, with the number of alleles per locus ranging from two to six, and an average of 3.38 alleles per locus. Observed and expected heterozygosity ranged from 0.143 to 0.786 and 0.138 and 0.751, respectively. Paternity exclusion probability was high (&gt; 0.999), and the probability of identity was low (2.05 × 10^− 8). The new set of 16 polymorphic STRs described here are now available to be used by Brazilian authorities for inspection and forensic purposes. Besides, it will contribute to assessment of the genetic diversity, population structure and planning of conservation actions of <i>A. leari</i>, and possibly other closely related macaw species.</p>