The common coquí (Eleutherodactylus coqui) is a culturally and ecologically significant amphibian endemic to Puerto Rico, yet genetic information for native populations remains limited. This study aims to assess intraspecific genetic variability in E. coqui using mitochondrial COI DNA barcoding obtained exclusively through non-invasive sampling methods. The results will establish a local genetic reference and support future research on population structure, conservation, and management of Puerto Rican amphibians.