Amphibians are among the most vulnerable vertebrates, with 41% of assessed species at risk of extinction. The genus Oophaga has most of its species currently listed as threatened by the IUCN. Oophaga vicentei, an endangered species endemic to central Panama, is facing strong pressures from habitat fragmentation and mining. Despite its threat status, little is known about its population structure and size. Reduced representation approaches are cost efficient alternative to obtain genome-wide estimates of genetic diversity in non-model species. We herein genotyped thousands of exonic SNPs using RNA-seq data to uncover the genetic structure and effective population size of O. vicentei.