In this study, the amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity of three populations of Pomacea canaliculata from Jiangsu, Fujian and Guangdong regions. A total of 369 polymorphic loci out of the total of 382 bands were amplified from 90 individuals. The proportion of polymorphic loci were 84.82%, 85.08%, 79.06% and Shannon′s Information index were 0.4259, 0.4308, 0.4079 in Jiangsu, Fujian and Guangdong population, respectively. These showed that there were high genetic diversity in all the three populations and the genetic diversity of three populations were in the same level. Shannon′s Information index and AMOVA analysis indicated that the genetic variation mainly came from intra\|populations. The UPGMA tree based on AFLP data demonstrated that each population had independent genetic structure——individuals from the same population clustered together, Guangdong population and Fujian population first jointed, then Jiangsu population. In addition, the population specific loci were found in all the three populations which could be used as markers for inter\|population molecular characterization and to assist the classification in P. canaliculata.