To determine the character of 18S rRNA V4 hypervariable region on taxonomic and taxonomic status of Theileria equi,the genes were compared with piroplasmida.According to 18S rRNA gene sequences of Theileria equi and Babesia caballi in GenBank,the primers were designed and were amplified by PCR.This sequences were cloned into pMD19-T vector and sequenced.The phylogenetic tree was structured about the sequence and other protozoan 18S rRNA V4 hypervariable region nucleotide sequence in GenBank.Theileria and Babesia are in different branches,but as Babesia equi has a relatively close relationship with the Theileria.Sequence alignment analysis showed,18S rRNA V4 hypervariable region has multiple deletion and mutation between Theileria and Babesia.The deletion and mutation can be used for Theileria and Babesia classification.So B.equi should be classified as Theileriidae,Theileria.