Abstract: To examine the systematic classification of four previously-recorded Daphnia species, D. carinata, D. hyalina, D. pulex, and D. magna, genomic DNAs of these species were extracted and PCR was used to amplify fragments of 16S rDNA and COⅠ gene by employing specific primers. The sequences of amplified fragments were compared with Daphnia species from the GeneBank. Based on 16S rDNA and COⅠ gene, the average interspecific similarity rate of four Daphnia species was 85.25% and 80.67% respectively, and the content of A+T was obviously higher than that of G+C. The similarity of D. carinata from Lake chaohu and D. similoides (AB549199) from the GeneBank was 99% according to COⅠ gene and the divergence rate was 0.4%0.9%. D. hyalina from Lake Chaohu was more close to D. galeata from the GeneBank based on 16S rDNA or COⅠgene. Main branches of both NJ tree and bayes tree were similar. The results indicated that D. carinata and D. similoides were the same species, and D. hyalina belongs to D. galeata. Due to the lack of nuclear gene analysis, the classification status of Daphnia species in Lake Chaohu needs further investigation.