Populations genetic studies are efficient to reveal the genetic consequence and evolution in local populations by comparing the genetic variability with the source populations. Introduced populations are typically thought to have a geographically more uniform genetic structure than their source populations. Here we showed an opposite case that populations of Sinotaia cf. quadrata, a common freshwater snail distributed in Asia, with stronger genetic structure in Japan were introduced from weak structured populations in China. Genetic diversity was lower in the populations of Japan than in the continental populations. However, the genetic divergence among populations was higher in Japan than on the Asian continent. We attributed that different level of passive dispersal fostered by different human activities could be the dominant factor to influence the gene flow and population structures in the two regions. Our genetic analyses confirmed that the freshwater snail was introduced from Asian continent to Japan during historical periods. We assumed that introduction would be a multiple approach, but still could not stop the genetic differentiation in Japan. Our results suggest that human activities driven by cultural differences play a dominant role in shaping the distinctive population structure between introduced and source populations.