ABSTRACTThe speciesBabesia microti, commonly found in rodents, demonstrates a high degree of genetic diversity. Three lineages, U.S., Kobe, and Hobetsu, are known to have zoonotic potential, but their tick vector(s) in Japan remains to be elucidated. We conducted a field investigation at Nemuro on Hokkaido Island and at Sumoto on Awaji Island, where up to two of the three lineages occur with similar frequencies in reservoirs. By flagging vegetation at these spots and surrounding areas, 4,010 ticks, comprising six species, were collected. A nested PCR that detects the 18S rRNA gene ofBabesiaspecies revealed thatIxodes ovatusandI. persulcatusalone were positive. Lineage-specific PCR for rRNA-positive samples demonstrated thatI. ovatusandI. persulcatuscarried, respectively, the Hobetsu and U.S. parasites. No Kobe-specific DNA was detected. InfectedI. ovatusticks were found at multiple sites, including Nemuro and Sumoto, with minimum infection rates (MIR) of ∼12.3%. However, allI. persulcatusticks collected within the same regions, a total of 535, were negative for the Hobetsu lineage, indicating thatI. ovatus, but notI. persulcatus, was the vector for the lineage. At Nemuro, U.S. lineage was detected in 2 of 139 adultI. persulcatusticks (MIR, 1.4%), for the first time, while 48 ofI. ovatusticks were negative for that lineage. Laboratory experiments confirmed the transmission of Hobetsu and U.S. parasites to hamsters viaI. ovatusandI. persulcatus, respectively. Differences in vector capacity shown by MIRs at Nemuro, where the two species were equally likely to acquire either lineage of parasite, may explain the difference in distribution of Hobetsu throughout Japan and U.S. taxa in Nemuro. These findings are of importance in the assessment of the regional risk for babesiosis in humans.