Amphibians represent the most threatened vertebrate class at risk of extinction. The most vulnerable species of this group can be found in small geographic areas, which increases their susceptibility to extinction. From the genus Agalychnis, the red-eye tree frog (Agalychnis callidryas) and the lemur tree frog (Agalychnis lemur) are closely related species native to Central America. While these frogs can be found in the same range, they are impacted differently by the emerging threats they both face. The IUCN lists the red-eye tree frog as a species of least concern and the lemur tree frog as critically endangered. Identifying specific reasons for their different statuses will be vital to saving the lemur tree frog and other declining species. The skin microbiome, a symbiotic complex of prokaryotic and eukaryotic microbes, plays important roles in maintaining host health, mitigating disease, and improving success with captive populations reintroduced to the wild. This study aimed to characterize and compare the skin microbiomes of these two closely related species of frogs from the tropical rainforest of Costa Rica and a captive setting. Frogs were swabbed from a private reserve in Costa Rica and two captive research colonies. The skin microbiomes were characterized using next-generation sequencing. Captive populations were found to have significantly different beta-diversity, suggesting species differences occur even under the same captive conditions. This study represents the first attempt at characterizing the skin microbiomes of these closely related anuran species in captive and wild settings