1. The Yaqui catfish, Ictalurus pricei, is the only native ictalurid species described from north-west México and south-west USA. It is an endangered species owing to the decline and loss of most of its historical populations, mainly because of competition and hybridization with the non-native channel catfish, Ictalurus punctatus. The Arroyo Caj on Bonito is one of the few remnant populations of Yaqui catfish in the Yaqui River basin, and it is threatened by the presence of channel catfish that escaped from private culture facilities.2. Phylogenetic analysis of two mitochondrial and two nuclear genes was used to detect evidence of hybridization with channel catfish in a collection of 20 catfish from Arroyo Caj on Bonito. Fourteen putatively pure Yaqui catfishes, five hybrids and one channel catfish were detected.3. This study further highlights hybridization between channel and Yaqui catfish as the main threat to the remaining Yaqui catfish populations. We recommend urgent evaluation of the remnant populations of native catfish elsewhere and their current conservation status.