The genetic diversity of silver carp (Hypophthalmichthys molitrix) populations around the world was thoroughly evaluated by AFLP at three different levels: populations within Yangtze River(Hanjiangsection, YZHJ and Laohesection, YZLH), among Chinese native populations(Yangtze River, YZ, Pearl River, PR overseas Amur River, AMU) and between Chinese native populations and overseas transplanted populations (Danube River, DAU and Mississippi River, MIS). The results showed Nei’s genetic diversity (H) of native populations was 0.048 1±0.115 1, 0.065 9±0.133 3, 0.051 0±0.115 5, 0.066 1±0.136 4 for YZHJ, YZLH, PR, AMU, respectively; while it was 0.057 6±0.125 0, 0.054 0±0.122 1 for the transplanted populations of DAU and MIS, respectively. The whole genetic diversity of the Chinese native populations(0.072 9±0.129 5) was higher than that of the transplanted populations. AMOVA showed the variance within population(91.86%) was larger than that of interpopulation(8.14%). The genteic divergence index within Yangtze River group, Chinese native groups, Chinese native groups and overseas groups was 0.070 1(P<0.01), 0.070 4(P<0.01) and 0.042 4(P<0.01), respective, which showed there are significant differences in three different group levels. These results would lay a base for long observation on trend of genetic variation of silver carp native populations and transplanted populations.