PCR-DGGE fingerprinting was explored in the present study to analyze intestinal contents of filterfeeding fishes (Hypophthalmichthys molirix and Aristichthys nobilis), which were sampled from the Donghu Lake, Wuhan. Different microbial bands (16S rDNA) and eukaryotic bands (18S rDNA) were detected in all the individuals, and the numbers of 16S rDNA bands were more than that of 18S rDNA bands. Results of the present study suggested that it is possible and useful to apply PCR-DGGE fingerprinting to studying the intestinal contents of filterfeeding fishes. Additionally, PCR-DGGE fingerprinting and sequences analysis of the DGGE bands indicated that intestinal contents composition of silver carp and bighead carp, which had been found to be significantly different in traditional dietary analyses with microscopy identification, was not significantly different. These results suggested that a significant portion of planktonic organisms were fed by the silver carp and bighead carp. In DNA based dietary analyses, multiple samples can be studied simultaneously with a standardized set of procedures, making it practical to perform comparative analyses, and furthermore, this comparison makes it possible to elucidate some objective ecological rules.