Genetic diversity of cultivated Crassostrea angulata in coastal sea of Fujian was analyzed by amplified fragment length polymorphism (AFLP). A total of 331 loci reproducible bands amplified with four AFLP primer combinations were assessed from 239 individuals in the eight domestic populations including four natural seeding cultivated populations and four artificial breeding populations, of which 233 (70.39%) were polymorphic. The proportion of polymorphic loci, the Nei’s gene diversity and Shannon’s Information Index of 8 cultivated populations were 57.10%-69.54%, 0.196 7-0.249 2, 0.290 2-0.362 6, respectively. Gst value and the AMOVA analysis indicated that the genetic variation mainly came from different individuals within the population. Cluster analysis based on UPGMA and PCA showed that genetic variation occurred within groups for each population, and there was no distinct boundary within the four natural seeding populations. Results showed that the genetic diversity of natural seeding cultivated populations had higher genetic diversity compared with artificial breeding cultivated populations, and a certain degree of genetic differentiation among populations was observed.