For resolution of the controversial taxonomic status of Babesia microti in relation to other Babesia and Theileria spp. a phylogenetic analysis of an American and a German B. microti strain was performed on the basis of sequences of the small-subunit rRNA gene (rDNA) using distance-matrix, maximum-parsimony, and maximum-likelihood algorithms. Both B. microti isolates clearly separated from a group containing other Babesia spp. as well as from a second group consisting of Theileria spp. Interestingly, the B. microti isolates clustered in a monophyletic group together with other piroplasm species of unclear taxonomic status, B. rodhaini, and a recently described small canine piroplasm species. These results support the existence of a third taxonomic entity of equal rank besides the Babesiidae and Theileriidae.