Endemic spotted fever group rickettsiosis was reported in Shimane Prefecture, Japan. From an analysis of 14 clinical cases found in the endemic area, the infectious agent of spotted fever group rickettsiosis was identified as Rickettsia japonica. In this study, we also found that Rickettsia japonica was highly infected with the vector tick, Haemaphysalis longicornis, in the endemic area. These findings suggest that the high incidence of rickettsiosis in Shimane Prefecture can be explained by the high prevalence of Rickettsia japonica among Haemaphysalis longicornis ticks.