Abstract: Genetic segregation of AFLP markers in three Pinctada fucata families, i.e. Indian family (Indian♀ Indian♂, PII), hybrid family (Sanya♀Indian♂, PSI) and Sanya family (Sanya♀Sanya♂, PSS) as well as their genetic variation was investigated. Three pairs of primers generated 57 loci, among which 57.4%~87.7% were segregated in F1. The proportion of loci segregated in Mendelian ratio over segregated loci ranged from 70.0% to 71.0%, of which 24.0%~45.2% segregated in 1∶1 ratio. Hybrid family had the highest ratio of 1∶1 segregating markers. The proportion of polymorphic loci was 93.0%~100.0% for the three families using 0.95 criterion. An overall genetic diversity (HT) was 0.460 and within-family genetic diversities (hS) were 0.434，0.331，0.366 for families PII，PSI，PSS, respectively, with an average of 0.3770.030 (HS). Genetic differentiation among the three families was significant (GST=0.180). Analysis of genetic distances showed that Sanya family PSS was most distant from hybrid family PSI (0.157) while nearest to the Indian family PII (0.121). The UPGMA tree indicated that the two pure families PII and PSS were closely related and grouped together. These observations indicated that genetic variation in F1 family is high while genetic differentiation among families is great and significant. These findings shall be useful in management of genetic resources during breeding of pearl oysters.