To carry out genetic evaluation on growth traits in redfin puffer (Takifugu rubripes) by using molecular marker-assisted family selection and breeding, in this study, the mature 11 females and 11 males chosen from the selection and breeding founder were used to produce 11 full-sib families of redfin puffer. 10 individuals from each family separately raised were random selected to construct the family population. About 400 larger individuals from the families raised together were random selected to construct the mixed breeding population. A set of 44 microsatellite DNA markers distributed evenly in 22 linkage groups were selected from the genetic linkage maps of redfin puffer, furthermore, 2 markers were located in each linkage group. According to the Excl 1 and Excl 2 probabilities based on the results of genetic analysis in full-sib family population, high probability values of 10 markers ranged from 0.58 to 0.662 and 0.736 to 0.797, low probability values of 14 markers were from 0.054 to 0.43and 0.177 to 0.608, and intermediate probability values of the remainder 20 markers showed 0.467 to 0.575 and 0.641 to 0.732. The results of parentage determination of mixed breeding population by using these markers with higher parental probabilities demonstrated that there were differences in the number of offspring from the combination of different parents. Male M2 and female F4 generated 124 offspring, whose percentage of all the individuals attained to 32.89%. Estimating the genetic parameters of growth traits with the marker-based pedigree according to the results of parentage determination, the heritabilities of body weight and body length were from 0.17 to 0.21 and 0.15 to 0.18 at different days of age, respectively. The research results verified that the microsatellite DNA markers selected with higher parental probabilities of exclusion can effectively construct the pedigree in redfin puffer to perform the estimation of genetic parameters for growth traits, therefore, molecular marker-assisted family selection is an efficient approach to genetically improve objective traits in this species.