| Wild rock Carps (Procypris rabaudi) were captured from Hejiang and Mudong regions of the Yangtze River, Cangxi and Beibei regions of of the Jialing River, Tongjiang region of the Qujiang River, and branches of the Yangtze River,the Xishui River and Tanghe River in 2002-2005. Artificially propagated rock carps were sampled from Sichuan Fisheries Research institute and Chongqing Wanzhou Fisheries Research institute in 2004-2005. The genetic diversity of the wild and artificially propagated populations was examined using AFLP markers and mitochondrial DNA control region. The results are as follows.A total of 386 loci were amplified using 6 AFLP primer combinations in 70 individuals of rock carps, of which 85. 49% were polymorphic. The population with the highest percentage of polymorphic loci was Hejiang population (67.88%), and the population with the lowest percentage of polymorphic loci was Wanzhou artificially propagated stock (24.09%). The average genetic distance among 8 populations was 0.1230 (0.0285-0.2260). The genetic distance between Beibei population and Yibin artificially propagated stock was the highest (0.2260), while that between Tongjiang population and Hejiang population was the lowest (0.0285). The average genetic distance, 0. 3056 (0.0951—0.4963) , among individuals in Mudong population was the highest and that of population Wanzhou, 0. 1401 (0.0614—0.2225), was the lowest. The UPGAMA dendrogram showed that the 8 populations could be clustered into 2 branches, one including the six wild populations, and the other including the two artificial propagated populations. The average heterozygosity among 8 populations was 0.2816. The population with the highest heterozygosity was Xishui, and the population with the lowest heterozygosity was Wanzhou.The estimated Fst value averaged over all polymorphic loci was 0.2993, indicating a moderate degree of genetic differentiation among the populations.
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