Abstract: Silver carp(Hypophthalmichthys molitrix Cuvier et Valenciennes)and grass carp(Ctenopharyngodon idellus Cuvier ct Valenciennes)are the most important farmed fishes in China. The seedlings of said species for aquaculture have came directly and indirectly from the Yangtze River because germplasm resources of silver carp and grass carp in this river is superior to those of other rivers. Therefore. genetic resources of silver carp and grass carp in the Yangtze River play a very important role in fisherics development in China in the long run. In present study, using RAPD(random amplified polymorphic DNA)technique we analyzed four populations. Two of them. namely, Jia-yu and Rui-chang which are from the middle reaches of Yangtze River, and the other two populations. namely, Han River and Xiang River which are from two branches of the middle reaches of the Yangtze River. Generally, genetic diversity in silver carp is higher than that of grass carp, but biomass of grass carp is higher than that of silver carp in the Yangtze River. The genetic diversity and biomass have negative relation, which is not consistent with most cases. The genetic diversity from highest to lowest in populations of silver carp is Jia-yu, Xiang River, Rui-chang and Han River population whereas in grass carp the genetic diversity from highest to lowest is Rui-chang. Han River. Xiang River and Jia-yu population. The population relationships of two specics are not consistent with each other. Gst for silver carp and grass carp is 12.3% and 17.5%, respectively, which indicated that genetic differentiation among populations in said two species is low. The reason for low genetic differentiation and population relationship may be due to sampling location, which are close to each other. The other reason may be due to frequent gene flow among populations.