A recent increase in the occurrence of canine skin and soft tissue infections, including otitis externa and pyoderma, caused by antimicrobial-resistant Staphylococcus pseudintermedius and S. schleiferi has become a significant public and veterinary health issues. We investigated the virulence potentials associated with the occurrence of canine otitis externa in S. pseudintermedius and S. schleiferi. In this study, the prevalence of genes encoding leukocidins, exfoliative toxins, and staphylococcal enterotoxins (SEs) was investigated using previously characterized S. pseudintermedius (n = 26) and S. schleiferi (n = 19) isolates derived from canine otitis externa. Susceptibility to cathelicidins (K9CATH and PMAP-36) and hydrogen peroxide (H2O2) was also examined in both staphylococcal species. A high prevalence of genes encoding leukocidins (lukS/F-I, lukS1/F1-S, and lukS2/F2-S), exfoliative toxins (siet, expB, and sset), and SEs was identified in both S. pseudintermedius and S. schleiferi isolates. Notably, S. pseudintermedius isolates possessed higher number of SE genes, especially newer SE genes, than S. schleiferi isolates harboring egc clusters. Although no significant differences in susceptibility to K9CATH and H2O2 were observed between the two isolate groups, S. pseudintermedius isolates exhibited enhanced resistance to PMAP-36 compared to S. schleiferi isolates. These findings suggest that high a prevalence of various toxin genes together with enhanced resistance to cathelicidins may contribute to the pathogenicity of S. pseudintermedius and S. schleiferi in canine cutaneous infections.