Simple Sequence Repeat(SSR)and inter-simple sequence repeat (ISSR) markers were applied to measure the genetic variation and genetic structure of the selected stock (SH) and wild population (YS) of Takifugu flavidus. Results of SSR showed that a total of 146 alleles were detected among 60 individuals with 14 polymorphic microsatellite loci, and the mean of expected heterozygosity (He) and polymorphism information content (PIC) of two populations ranged from 0.730 0 to 0.832 3 and from 0.705 1 to 0.813 6, respectively. The analysis of ISSR showed that the average Nei's gene diversity index (H) of selected stock and wild population were 0.267 2 and 0.282 3, respectively, while the average Shannon information index (I) of two populations were 0.407 2 and 0.425 6, respectively. These results showed that the genetic variation of wild population was higher than that of the selected population of Takifugu flavidus. Additionally, genetic differentiation coefficient (F_ST) value between the two populations of Takifugu flavidus were 0.061 9 (SSR) and 0.061 5 (ISSR), which indicated that two populations generated moderate genetic differentiation. These results above indicated that the selective breeding stock of Takifugu flavidus still possessed abundant genetic variation at population level, and had great potential for artificial selection and breeding.