Abstract: Mitochondria1 control （D-Loop ）region and cytochrome b (Cyt b) gene of Bronze gudgeon (Coreius heterodon) in the lower reaches of the Yangtze River were cloned by PCR . Cloned fragments were digested by ten kinds of restriction endonucleases . Result of PCR-RFLP showed that no length diversity among different individual were detected both in D-Loop region and Cyt b gene. Among ten restriction endonucleases, Cyt b gene could be digested by two kinds of those and D-Loop region could be digested by three kinds of those. Three kinds of haplotypes were detected with five enzymes. Diversity among individuals of Bronze gudgeon was detected in Cyt b gene , while no diversity was found among different individuals in D-Loop region. The haplotype diversity index of of Bronze gudgeon in the lower reaches of the Yangtze River was 0.6071,which revealed a lower genetic diversity in mtDNA.