Abstract: Silver carp(Hypophthalmichthys molitrix)and grass carp(Ctenopharyngodon idellus)are the most important farmed fishes in China. The seedlings of said species for aquaculture have come directly and indirectly from the Yangtze River because germplasm resources of silver carp and grass carp in the Yangtze 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 fisheries development in China in the long run. In present study, mitochondral DNA variations were screened in four populations of the middles reaches of the Yangtze River by using PCR RFLP method. The four populations include two populations, namely, Jiayu and Ruichang which are from the middle reaches of the Yangtze River, and the other two populations, namely, Han River and Xiang River which are from two branches of the middle reaches of Yangtze River. Eighteen haplotypes in silver carp are detected using ten restriction enzymes, including Rsa Ⅰ, Hae Ⅲ, Hinf Ⅰ, Hpa Ⅱ, Dde Ⅰ, Taq Ⅰ, Nci Ⅰ, Alu Ⅰ, Ava Ⅱ and Hinc Ⅱ. However, no genetic variation is noted in grass carp by using same enzymes. Obviously, the genetic diversity in grass carp is much poor than that of silver carp in the middle reaches of the Yangtze River. The genetic diversity and biomass has negative relation, which is not consistent with most cases.