Infectious diseases have the potential to play a role in the decline of threatened wildlife populations, as well as negatively affect their long-term viability, but determining which infectious agents present risks can be difficult. The southern resident killer whale, Orcinus orca, population is endangered and little is known about infectious diseases in this species. Using available reference literature, we identified 15 infectious agents (bacteria, viruses, and fungi) reported in free-ranging and captive killer whales, as well as 28 additional infectious agents reported in free-ranging and captive odontocete species sympatric to southern resident killer whales. Infectious agents were scored as having a high, medium, or low ability to affect fecundity or reproductive success, to cause disease in individual animals, and to cause epizootics. Marine Brucella spp., cetacean poxvirus, cetacean morbilliviruses, and herpesviruses were identified as high priority pathogens that warrant further study. Using identified pathogens to develop a standardized necropsy and disease testing protocol for southern resident killer whales and sympatric odontocetes will improve future efforts to better understand the impacts of priority and non-priority infectious agents on southern resident killer whales. This model can be used to evaluate potential infectious disease risks in other threatened wildlife populations.