Abstract: ISSR,the inter-simple sequence repeats was applied to investigate the genetic diversities of three wild population ofpearl oyster; Pinctada martensii (Dunker),the wild populations fromBeihai (BW),Daya Bay (DW) and Sanya (SW). The geneticdiversity index of BW,DW and SW were 0.2585,0.2607 and 0.2571 respectively. Three first generations of hybridization be2tween wild population were produced,BD1,from BW and DW,BS1 from BW and SW,DS1 from DW and SW. At the same time,three first generations of mating in each wild population were also produced,BB1 from BW,DD1 from DW,and SS1 from SW. Thegenetic diversity index of hybridizing generation,BD1,BS1 and SD1 was 012659,012747 and 0.2784 respectively. BB1,DD1 andSS1 had its diversity index,which was 0.2504,0.2527 and 0.2545. To get heterosis from hybridization between populations,ge2netic traits of parents need to be purified. Genetic diversity in self2mating population was lower than that of corresponding wildpopulation. It suggested that keeping effective population size was very important to avoid inbreeding in cultured breeding and se-lective breeding.