Abstract: Collecting wild mud carp population from the section of Zhaoqing, Xijiang River, Guangdong Province, succeeding observation, and recording morphological parameters, the results showed that two different stocks appeared in the river. Of the two, one with body color of light yellow were named after h, the other with body color of cyan named after q .The growth performance of stock h was better than stock q. Random amplified polymorphic DNA( RAPD) technique was applied to assess the genetic variations of the two stocks, 24 individuals respectively. Amplifications with 20 random primers gave 179 reproducible and stable fragments and 82 fragments of which was polymorphic. Based on RAPD data, the mean heterozygosity and genetic distance of the whole population was 0.1281 and 0.1232, the mean heterozygosity and genetic distance of stock h were 0.1248 and 0.1151, the mean heterozygosity and genetic distance of stock q were 0.1164 and 0.1010. The genetic distance between the two stocks was 0.1383. The results of RAPD analysis indicated that the genetic diversity of the original breed was relatively high.