We report the discovery of a population of Trachemys grayi emolli in southern Honduras. Verification of the species was based on both morphological and molecular data (ND4, COI, ctyb). We discuss problems that arise from the use of sequences from nonvouchered pet trade and turtle farm samples for inferring phylogenetic relationships and confirming species identifications. We postulate that incongruence between mitochondrial and nuclear trees may relate to introgressive hybridisation amongst captive animals. This highlights the dangers of using pet trade specimens of uncertain origin and potential hybrid status in molecular phylogenetic studies.