Theileria and Babesia are tick-transmitted protozoa that cause great economical losses in livestock. Recently, interest has risen in sheep-infecting piroplasms and a number of previously unidentified pathogens were described, particularly in China. To address the phylogenetic relationship of Theileria and Babesia species infecting sheep, the complete sequences of the 18 S small subunit ribosomal RNA genes of a panel of piroplasm isolates, including T. lestoquardi, T. ovis, T. separata, B. ovis, B. motasi, B. crassa, and several novel species, were compared. The classification based on the established phylogenetic tree corresponded with traditional systematics and revealed that sheep/goat piroplasm species are of a polyphyletic origin. In addition, these studies revealed the existence of at least two novel sheep/goat piroplasm species, designated Theileria sp. (China 1) and Theileria sp. (China 2).