Aims: To examine the community structure of cyanobacterial populations of the South China Sea on the surface and at depth of 80 m. Methods and Results: Direct PCR amplification of RNA polymerase (rpoC1) genes from environmental DNAs extracted from seawater, and cloning of the fragments and sequence analysis were used. A great diversity of Prochlorococcus and ynechococcus were detected at the investigation site. Genetically related Prochlorococcus were found in both layers while Synechococcus were found only on the surface. Prochlorococcus were clustered with the known high-light adapted II genotypes, and further divided into seven groups. Synechococcus could be divided into two groups, and the second group could be further subdivided into several clades. Conclusion: The dominant genotype of Prochlorococcus was high-light adapted II genotype, and Synechococcus were distributed basically on the surface. Significance and Impact of the Study: This is the first report about the cyanobacterial community structure in the South China Sea, and an important supplement to the current understanding of the relationship between genetic and ecological diversity and environments.

Accurate quantification of aerobic anoxygenic phototrophic bacteria (AAPB) is of crucial importance for estimation of the role of AAPB in the carbon cycling in marine ecosystems. The normally used method "epifluo-rescence microscope-infrared photography (EFM-IRP)" is, however, subject to positive errors introduced by mis-taking cyanobacteria as AAPB due to the visibility of cyanobacteria under infrared photographic conditions for AAPB. This error could be up to 30% in the coast of the East China Sea. Such bias should be avoided by either ubtracting cyanobacteira from the total infrared counts or using a flowcytometer equipped with specific detectors for discrimination between cyanobacteria and AAPB.