Babesia divergens is the major causal agent of zoonotic human babesiosis across Europe. Previously, we reported the detection of a B. divergens Asia lineage in wild sika deer (Cervus nippon) in Japan which was genetically closely related to the European B. divergens. To further elucidate its etiology, we conducted a large epidemiological survey by combining lineage-specific PCR system and blood direct PCR. The infection rate of the Asia lineage was 6.6% (116/1,747) throughout Japan, where Hokkaido (45%), Nagano (17%), Iwate (12%), Gunma (11%), and Yamanashi (11%) were highly enzootic (> 10%) among the 30 prefectures examined. European B. divergens was not detected. A geographical information system (GIS) map revealed dense populations of PCR-positive deer in the mountains including the Japanese Alps in eastern Honshu, and Hokkaido. These areas markedly overlapped with the major habitats of Ixodes persulcatus, a principal tick vector responsible for the transmission of the Asia lineage. Other areas in southern Japan including Miyazaki, Kagoshima, and Shimane Prefectures, where positive sika deer were sporadically detected, may be habitats for other tick species involved in the enzootic cycle as I. persulcatus were scarce. The rise in human babesiosis cases is occasionally attributed to healthy blood donors who were unaware of tick bites and Babesia infection. Therefore, there is an urgent need to investigate whether infections in humans have occurred in Japan.