The present study was designed to explore relationship between DNA polymorphism, as revealed by RAPD and PCR-DGGE fingerprintings, and species composition of plankton community in an artificial lake for breeding transgenic fish. Planktonic samples were collected from five sampling sites in the artificial lake, and their similarity was assessed with cluster analysis. The results were: (1) a total of 44 planktonic taxa were identified, among which there were 13 algae, 11 protozoa, 16 rotifer, 2 Cladocera and Copepoda, respectively; (2) 128 observable bands were totally amplified by the 9 random primers screened in RAPD analysis, among which 61.7% and 19.5% were polymorphic bands and specific bands, respectively; (3) there were 87 distinct bands identified by the method of PCR-DGGE, among which 50 were 16S rRNA bands and 37 were 18S rRNA bands. Despite the analysis of morphological identification and DNA fingerprintings had shown a higher species diversity, the cluster of similarity was different: based on species composition, group 1 consisted of B, C sites, group 2 contained D, E sites, and group 3 only comprised of A site. However, according to the DNA fingerprint analysis, the plankton community of C, D, E were similar, and another two sites-A and B were similar. In summary, our results suggested that the species composition was not closely related to the DNA polymorphism of plankton community, and the latter can describe more species. However, the characteristics of biodiversity revealed from different ), 2009, 21(3) 376 a