Partial portions of ND4 and ND5 genes from Brachionus caudatus, B. diversicornis, B. forficula, B. quadridentatus, B. rubens, B. falcatus, B. leydigi, B. patulus were amplified and sequenced. Combined with ND4 and ND5 genes of B. plicatilis, B. calyciflorus, Rotaria rotatoria and Philodina citrina from GenBank, phylogenetic trees of neighbor-joining (NJ), minimum-evolution (ME) and unweighted pair-group method using an arithmetic average (UPGMA) methods were built with MEGA6.0 software to reveal their phylogenetic relationships and resolve some taxonomy problems. The results showed that the average percentage of divergence for ND4 and ND5 genes sequences in 12 samples was 40.3%. ND4 and ND5 genes were suitable for researching the phylogenesis and evolution of rotifera species in the genus. The relationships of Brachionus showing from the phylogenetic trees were basically consistent with morphological studies. All the three trees showed that B. patulus and B. diversicornis were confirmed to belong to the genus Brachionus.