Bushmeat hunting and consumption, although widely utilized as necessary supplement to household income and nutrition in many regions, presents threats to public health and wildlife conservation efforts. In northern Uganda, consumption of bats and primates, two wildlife groups often implicated in zoonotic disease emergence, is not widely culturally accepted; however, these species are reported by hunters to often be hunted and sold as culturally desirable species, like antelope and warthog. To investigate the prevalence of market bushmeat misidentifiction, we collected 229 bushmeat samples from 23 communities adjacent to Murchison Falls National Park. Reported species was recorded on acquisition for each sample. PCR targeting mammalian cyt b and 12 s rRNA genes and sequencing were performed to identify samples to the lowest taxonomic unit using NCBI BLAST. Overall, 27.9% (61/219) of samples had disparate results between species reported and BLAST analysis. Thirty-four species were identified, with the most frequent wildlife being waterbuck (31.5%), warthog (13.7%), and black rat (5.9%). These data reveal a public health risk for bushmeat consumers in northern Uganda as they cannot assess species-related risk when purchasing bushmeat and take appropriate precautions against zoonotic pathogen exposure. These data also provide insight into regional hunter prey preference and market preference of local community members which may inform conservation strategy in the region.