The bacterial composition along the intestinal tract of Danio rerio was investigated by cultivation-independent analysis of the 16S rRNA gene. Clone libraries were constructed for three compartments of the intestinal tract of individual fish. 566 individual clones were differentiated by amplified 16S rRNA gene restriction analysis (ARDRA), and clone representatives from each operational taxonomic unit (OTU) were sequenced. As reported in other studies, we found that Proteobacteria was the most prominent phylum among clone libraries from different fish. Data generated from this pilot study indicated some compositional differences in bacterial communities. Two dominant classes, Gammaproteobacteria and Bacilli, displayed different levels of abundance in different compartments; Gammaproteobacteria increased along the intestinal tract, while Bacilli decreased its abundance along the proximal-distal axis. Less obvious spatial patterns were observed for other classes. In general, bacterial diversity in the intestinal bulb was greater than that in the posterior intestine. Interindividual differences in bacterial diversity and composition were also noted in this study.