Abstract: To explore the potential relationship between differentiation of gastrointestinal tract and the gastrointestinal microbiota colonization, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was applied to analyze the gastrointestinal microbiota alteration of Silurus soldatovi meridonalis Chen with the differentiation of gastrointestinal tract. The differentiation of the intestinal microbiota started from 18-day samples and kept relatively stable in the following 23-, 28- and 33-day samples. However, the differentiation of the stomach microbiota was in dynamic variation process during the experiment. Morphological observation and histological slices of the gastrointestinal tract suggested a significant differentiation started at the developmental stage of 13-day. It indicated that with the differentiation of digestive system, the differentiations of bacteria community structures of both stomach and gut were different in spatiotempord.