This study was aimed to construct the genetic linkage mapping in Takifugu snydri and to identify sex-determining region. Three families (Family A, B, and C) of T. snyderi, were produced between three wild males and a single wild female caught at Suruga Bay, Shizuoka Prefecture, Japan. Procedures for artificial fertilization and rearing condition were set according to the Fisheries Laboratory protocol. The GRAS-Di technology was used to obtain the genome-wide genotype data from 98 fish from Family A with their parents. We used these GRAS-Di data to construct male and female genetic linkage map of Takifugu snyderi, and finally QTL analysis was done to identify the sex determining locus.