Abstract: Heterotrophic bacterial community, in the surface sediment of Portunus trituberculatus rearing ponds with disease occurring and one without, was investigated by means of the morphology and 16S rDNA sequences. A total of 255 isolates were roughly clustered into 13 colony-based groups and 33 cell-based subgroups.The 16S rDNA sequences were analyzed of the two dominant subgroups A-NS-SpR (non spore-forming sphere-rod in A group) and B-SF-SR (spore-forming short-rod in B group), both of which accounted for 34.5% of all isolates. Subgroup A-NS-SpR belongs to phylum Proteobacteria, including two classes, three families, eight genara and about twelve species, and the dominant species are Halomonas ventosae and Donghicola eburneus, which totally accounted for 59.1% of this subgroup. Subgroup B-SF-SR belonges to phylum Firmicutes, including one class (Bacilli), three families, four genara and about twelve species. And two species (Bacillus decolorationis and Halobacillus trueperi) accounted for 60.6% in this subgroup, much more than other species. At genus level, Bacillus and Halomonas are majors within sbugroup. Subgroup A-NS-SpR show much higher abundance (number of isolates) in the healthy pond than in the diseased one, but similar diversity (number of species) with the latter. And family Rhodobacteraceae shows the biggest drop in the abundance in the diseased pond. In contrast, Subgroup B-SF-SR shows minor differences in abundance in healthy and diseased ones, but its diversity in the diseased pond lost obviously, compared with the healty one.