Neosalanx taihuensis is a small-sized freshwater fish from the Salangidae family, and is found mainly in the middle and lower reaches of the Yangtze River, including its tributaries and affiliated lakes. N. taihuensis has a high commercial value, and was therefore introduced to lakes and reservoirs in many Chinese provinces during the 1980s. It very rapidly adapted to the new conditions present in these lakes and reservoirs, quickly becoming the dominant species of fish. This caused a population decline in several native species, which led to notable changes in the community structure of fish and even local extinctions. It is currently understood that the level of genetic variation present in a population influences its ability to adapt to changing conditions. Therefore, in order to better understand the genetic mechanisms that allow N. taihuensis to successfully invade and adapt to new ecosystems, 10 microsatellite loci were performed to comparatively analyze population genetic structure of N. taihuensis between 5 invasive areas and 2 original areas. Genetic diversity parameters indicated that invasive populations from Dianchi Lake, Qionghai Lake, Fuxianhu Lake and Three Gorges reservoir had higher levels of genetic diversity than those living in original areas of Taihu Lake and Chaohu Lake, and invasive population from Erhai Lake had the lower level of genetic diversity than that from Taihu Lake, but higher level of genetic diversity than that from Chaohu Lake, whilst original area of Chaohu Lake had the lowest level of genetic diversity. The value of pairwise genetic distance was from 0.0062 to 0.1013. The genetic distance between Qionghai and Chaohu populations was the greatest, whilst the genetic distance between Taihu Lake and Fuxianhu Lake populations was the smallest. Both genetic distance and UPGMA clustering results showed that the Qionghai population had the farthest genetic relation with the other populations, whilst relationship between Taihu Lake and Fuxianhu Lake populations was the nearest. ANOVA analysis revealed most of the total variation occurred within populations (95.78%) and a small amount of differentiation among populations (4.22%). F_st value (0.0422) was significant, which exhibited a low and significant population differentiation. Out of 21 pairwise comparisons of populations, significant genetic divergence was detected in 18 pairs (85.7%) of populations, which also confirms the significant population differentiation. The value of F_st between Qionghai Lake and Chaohu Lake populations was maximum among all pairwise comparisons. Significant genetic differentiation was not found in three pairs of populations: Taihu Lake vs. Fuxianhu Lake, Taihu Lake vs. Erhai Lake and Fuxianhu Lake vs. Erhai Lake. MVSP principal component analysis demonstated the populations from Qionghai Lake, Three Gorges reservoir, Chaohu Lake and Dianchi Lake displayed a clear differentiation. It could conclude that high level of genetic diversity and the significant difference of genetic structure might be the important reasons for successful invasion of N. taihuensis.