Acquiring data on rare and threatened species can be challenging, particularly in remote areas. However, environmental DNA (eDNA) surveys offer a less effort-intensive method of detecting these species than more traditional fish sampling methods. In our study, we focused on the Yaqui Catfish (Ictalurus pricei), an endangered freshwater fish endemic to the Sonoran desert (Arizona, US and Sonora, Mexico), and the non-native Channel Catfish (Ictalurus punctatus). To detect these species, we developed and employed mitochondrial DNA markers and a stratified random sampling method. We collected water samples for eDNA detection from 35 locations in the Yaqui River basin in Mexico. Using a hierarchical Bayesian formulation of a co-occurrence model, we examined the effects of interacting species, where one species is dominant (Channel Catfish) and the other subordinate (Yaqui Catfish), while allowing for the effects of covariates to be specified on species occupancy and detection. Our best model included the influence of non-native Channel Catfish on detecting native Yaqui Catfish. Moreover, we found that detection of Channel Catfish was negatively related to water temperature and elevation, but positively related to substrate size. Occupancy of Yaqui Catfish was best explained by stream permanence (i.e., higher rates of stream discharge and low probabilities of the reach drying) and forested areas. Channel Catfish were also associated with stream permanence (i.e., low probabilities of the stream reach drying and larger upstream watershed areas) and conifer and shrub-dominated landscapes. Non-native Channel Catfish eDNA was found in all but five locations where Yaqui Catfish eDNA was detected, indicating a high likelihood of interaction and hybridization. The threat of hybridization to the already endangered Yaqui Catfish highlights the need to secure remaining populations for their long-term survival.