This epidemiological survey was conducted to determine the prevalence of Hepatozoon, Babesia and Theileria infection in the Iriomote cat (IC) and the Tsushima leopard cat (TLC). Blood samples from 43 ICs and 14 TLCs were collected between November 2002 and January 2012. Polymerase chain reaction and DNA sequencing analyses detected a Hepatozoon felis infection prevalence of 72.0% (31/43 cats) and 100% (14/14 cats) in ICs and TLCs, respectively. The degree of Hepatozoon parasitemia observed on blood smears ranged from 0.1 to 4.7%. However, no cases had obvious clinical signs of hepatozoonosis. Neither Babesia- nor Theileria-infected wildcats were detected in this study.