We present a mtDNA analysis of Podocnemis expansa (n 81) and Podocnemis unifilis (n 228) turtles traded in Peru to evaluate the potential origin of these animals. In particular, we were interested in the relationship between samples reported in the Iquitos markets (IMs) and a Pacaya Samiria Natural Reserve (PSNR) where illegal hunting is presumed. Our mtDNA data showed that, for both species, all haplotypes found within the PSNR were observed in the IM, and that these markets also displayed haplotypes not documented in the reserve. This suggests that the IMs are recipients of Podocnemis turtles from within and outside the PSNR. The fact that most of the haplotype diversity observed in the markets was not found within the PSNR strongly suggests that Podocnemis genetic diversity is exploited in areas where conservation actions are limited. Hence, we recommend expanding Podocnemis conservation efforts outside of protected areas.