Abstract: DNA was extracted and partial COⅠ was sequenced from water fleas Moina rectirostris using WizardTM genomicDNA purification kit,and the extracted DNA was used as a template in order to study the characteristics of mitochondrial cytochrome c oxidase subunit 1(COⅠ) in the water fleas.The sequence analysis revealed that the sequences had length of 709 bp,with 26.23% in A,19.89% in G,38.50% in T and 15.37% in C,and,higher in A + T(64.74%) than in G + C(35.26%).The phylogenetic tree was constructed with neighbor-joining of the six species by five species in Moinidae from the Gen Bank and the alignmented sequences.The results showed that the genetic distance between Moina rectirostris and Moina brachiata was the shortest,which belonged to a branch and the closest relationship.The genetic distance and NJ phylogenetic tree indicated that the species in Moinidae could be effectively separated,which was consistent with that by traditional morphological taxonomy.