Raptor pellets are regularly encountered in the field in a variety of habitats. Where multiple species of similar-sized raptors are sympatric, there can be uncertainty about which species produced a pellet based on visual assessments alone. We developed a DNA barcoding protocol that used environmental DNA (eDNA) to identify birds of prey that had produced pellets. Two different PCR primer pairs were required to successfully ascribe a pellet to the source bird species. Troubleshooting different suspension temperatures and applying multiple primer sets to the same eDNA sample provided sequences that successfully identified Red-tailed Hawk (Buteo jamaicensis) and Great Horned Owl (Bubo virginianus) pellets. Because eDNA degrades, this protocol will only work on pellets that have been in the environment for a limited time, probably <6 months.