The Iriomote cat (IC; Prionailurus iriomotensis) and the Tsushima leopard cat (TLC; Prionailurus bengalensis euptilura) are endangered wild felids in Japan. As a part of ongoing conservation activities, we conducted a molecular, epidemiologic survey of Bartonella, Ehrlichia, and Anaplasma infections in wild IC and TLC populations. Blood samples (47 from 33 individual IC; 22 from 13 TLC) were collected between August 2002 and January 2011. Using PCR analysis, we confirmed the presence of Bartonella henselae in ICs and Bartonella clarridgeiae in TLCs, with prevalences of 6% and 8%, respectively. Using PCR and basic local alignment search tool analyses, we identified Ehrlichia canis in both cats and Anaplasma bovis in TLCs. The prevalence of E. canis was 12% in ICs and 8% in TLCs, and the prevalence of A. bovis was 15% in TLCs. This is the first report, to our knowledge, of B. henselae, B. clarridgeiae, E. canis, and A. bovis infections in these two endangered species. Continuous monitoring of these pathogens is needed for their conservation.