We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models. Results showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical.