With the random amplified polymorphic DNA (RAPD) analysis method, forty ten-base arbitrary primers of OPJ and OPM groups were used to study the genetic variability among geographic stocks of Hyriopsis cumingii from the five large lakes of China: Po-yang Lake (PY), Dong-ting Lake (DT), Tai Lake(TH), Chao Lake (CH) and Hong-ze Lake (HZ), and one cultured stock from Zhuji City (ZJ) of Zhejiang Province. The amplified results of twelve primers showed abundant polymorphy, and the percentage of polymorphy with each primer amplified varied 55.6% to 80%. The intra-stock genetic similarity indexes ranked as PY(0.888 9)>TH (0.869 4)> DT ((0.811 1))> ZJ (0.774 6)> HZ(0.734 8)> CH(0.718 5). Based on inter-stock genetic distance indexes and molecular phylogenetic tree, we can conclude that the phylogeny relation between DT and HZ stocks is closest, and the cultured stock from ZJ is relatively close to the cluster of PY and CH stocks.