Neighbor-joining tree of Babesia microti inferred from the 1078 bp sequence of 18S rRNA gene using the Neighbor-joining algorithm method with the Kimura two-parameter model. The number on each branch denotes the percent occurrence in 1000 bootstrap replicates. Three genetically different B. microti variants, Yunnan-1, Yunnan-2 and Yunnan-3, were detected. Yunnan-1, Yunnan-2 and Yunnan-3 were associated with Rattus (11/49, 22·5%), Apodemus (10/13, 76·9%) and Crocidura (5/10, 50·0%) species, respectively.