Abstract: Grass carp (Ctenopharyngodon idellus) is one of the most important freshwater species in aquaculture. Meanwhile, the grass carp is originally distributes in China, and then it has been introduced into more than 100 countries for aquatic weed control and aquaculture since 1960s. In the past five decades, the grass carps have been adapted to the local environment and developed local groups. However, the genetic variation among the grass carps in native and introduced regions, aswell the genetic phylogeny, is not clear1Meanwhile, there is no available literature to clarifywhich river systems in China are the most likely origins of colonized populations in introduced regions1 In this study, partial sequences of the mitochondrial D-Loop (764bp), CO II + tRNA (719bp) were analyzed from native (the Yangtze, Amur and Pear.Rivers in China) and introduced (the Danube River in Hungary, theMississippi River in USA and the Tonegawa River in Japan) populations of the grass carp. The data of the two mtDNA fragments showed no competitive with the ILD (Incongruence Length Difference) test (p =0.42), and they could combine together as one data. The results indicated that there were the total of 32 haplotypes in all specimens, and 5 haplotypes were shared, all other haplotypes were singletons. In the 5 shared haplotypes, one was found in all populations, one in Amur River and Pearl River, two in China and Hungary, and the last one was found only in China. The genetic variation in the native populationswas higher than that in the colonized populations. In the native populations, the genetic diversity ordered as the Pearl Rivers (π=0.0042) > Yangtze River (π =0.0028)>Amur River (π = 0.0013). In the introduced populations, the genetic diversity ordered as the Danube River (π =0.0019) > Mississippi River (π =0.0010) > Tonegawa River (π =0.0001). The analysis of AMOVA using Arlequin 3.01 indicated that the variation mostly existed within populations (77.27%), but it was very low contribution from the sampling regions (0.38%). The pairwise FSTvalues demonstrated that there was a significant differentiation in most pairwise populations. The Tajima’s D values were significant negative in the populations of the Amur River andMississippi River (was marginable significance in Tonegawa River), which demonstrating the recent population expansion in their histories, and were positive in the other populations. Base on the software TCS 1.21, the haplotype network showed that the Yangtze River population would be the most original and then expanded to other rivers. Based on the base composition, transition/transversion values from the softwareMEGA4, the gene flow among populations using the software Migrate-2.4.3 showed that the Danube River population and the Tonegawa River population might have two origins from China, namely the Yangtze and Amur River, the Mississippi River population might have three origins, the Yangtze, Amur and Pearl Rivers. The gene flow gave a sign that all grass carp populations would be derived from the Yangtze River, which is agreement with the results of the haplotype network.