Dietary (scat) analysis is a key tool for assessing the potential effects of predators on prey and for comparing resource use between predators, information that is crucial for effective wildlife management. However, misidentification of the species from which scats originate could result in inaccurate conclusions regarding predator–prey interactions and their consequences for ecosystems, which may ultimately compromise conservation and management actions. To address this issue, we developed a framework for decision-making in the face of uncertain scat species origin by incorporating field, laboratory, and molecular identification techniques. We used the framework to examine the diets of two predators, a native apex predator (dingo, Canis lupus dingo) and an invasive mesopredator (feral cat, Felis catus), from 696 field-collected scats in the arid zone of Australia. We examined how uncertainty regarding scat species origin changed perceptions of the nature of the relationship between coexisting predators and their prey. The extent of dietary overlap between dingoes and cats varied with the method used to identify scat species origin. Dietary overlap assessed by laboratory identifications was twice as high as when uncertainty in scat species origin was resolved through our decision framework. If uncertainty in scat species origin is not resolved in dietary studies, practitioners and decision-makers relying on this information run the risk of making misinformed conclusions regarding the ecological function of predators (including potential impacts on threatened species), which could have perverse outcomes if the wrong predators are targeted for management. With uncertainty in scat species origin resolved through our decision framework, a low level of dietary overlap between the two predators was demonstrated, and medium-sized mammals most threatened with extinction were shown to be more at risk of impact from feral cat than from dingo depredations.