The clone library of 16S rDNA and the phylogenetic tree were constructed with extraction of bacterial DNA from seaweed bed sediment sample of Gouqi Island , PCR amplification of bacterial 16S rDNA by universal primers, molecular clone, sequencing of 16S rDNA fragments and sequence analysis. The biodiversity of bacteria and phylogenetic analysis showed that the bacterial community fell into five main lineages: Proteobacteria(48.2%), Firmicutes(22.2%), Actinobacteria(14.8%), Chloroflexi(3.7%), Acidobacteria(3.7%), In addition, a part of unidentified bacteria (7.4%) was detected. Gammaproteobacteria played the dominant role in the Proteobacteria community of the seaweed bed sediment, it was about 46.1%, followed by the Alphaproteobacteria（23.1%),Betaproteobacteria(15.4%), Epsilonproteobacteria(7.7%), Deltaproteobacteria(7.7%). As the preponderant bacteria of marine sediment, the composition of Proteobacteria community was different in dissimilar ecosystems. It explained that the composition of the functional group is closely related to the mechanism of ecosystem. As the two branches of Grampositive bacteria, Firmicutes and Actinobacteria mostly participated in decomposition of detritus and heterotrophic nutrient cycle in the seaweed beds of Gouqi Island.