Abstract: In this study, we applied PCR-DGGE fingerprinting to investigate the effects of refeeding on the diversity of intestinal microflora in allogynogenetic crucian carp. Fishes were reared in a semi-recirculating system until maturation at Institute of Hydrobiology. After the 30-day starvation, fishes were divided into two groups (the hungry group and the feed group). Three fishes were blindly selected from the hungry group for the extraction of the microbial DNA with the traditional Phenol-chloroform method. In the meanwhile, fishes in the feed group resumed to be fed. Three fishes in the feed group were blindly selected for extraction of the microbial DNA after 25 days. The PCR-generated bacterial DNA products were separated using a polyacrylamide gel as it exhibited increasingly higher concentrations of chemical de-naturant. Correspondence Analysis (CA) and clustering based on Jaccard index was used to analyze the similarity of the samples. The results showed that the feed group displayed less bands than the hungry group. There was significant difference in the deleted bands between the feed group (B1, B2, B5, B6, B7 and B23) and the hungry group (B11, B14, B16, B17 and B21), so we reasoned that the similarity of microflora between the two groups was low. The variance analysis showed that the variance within the feed group was larger than that within the hungry group. In conclusion, our results suggested that refeeding had strong effects on the diversity of intestinal microflora in allogynogenetic crucian carp.