Abstract: The partial mitochondrial COⅠ gene was sequenced from 40 individuals of four Brachionus species.The sequences were compared and their molecular phylogenetic trees were constructed by UPGMA,neighbor-joining and maximum parsimony methods using B.plicatilis as outgroup.The length of sequences was 543 bp,in which frequency of A+T was 65.3%,and a considerable variation of 157 nucleotide sites (28.9%) was detected.All of three trees suggested that B.quadridentatus is relatively closer to B.urceus than other species,and then to B.leydigi,last to B.calyciflorus.This result is consistent with that of traditional morphological taxonomy.