The ribosomal small-subunit RNA gene sequences of six Chinese Babesia stocks infective to cattle, including a Babesia bigemina isolate, a B. bovis isolate, two B. ovata isolates, a Babesia sp. Wenchuan isolate and a B. major isolate, were compared and analyzed. The target DNA segment was amplified by polymerase chain reaction and the product ligated into the pGEM-T Easy vector for sequencing. The length of the 18S rRNA gene of all Babesia species involved in this study varied between 1,653 and 1,693 bp. The phylogenetic trees were inferred based on the 18S rRNA sequence of the Chinese isolates as well as other species of Babesia available in GenBank. The results showed that the B. ovata transmitted by Haemaphysalis longicornis and Babesia sp. Wenchuan isolate were confined to the same group as B. ovata Korea, with an identity among them of >96.5%, while B. major transmitted by H. punctata was situated in another branch, and identity with other bovine Babesia species was less than 92.5%. B. ovata should, therefore, be a valid species, differing from B. major according to the 18S rRNA gene sequence.