Abstract: To develop reliable single nucleotide polymorphism (SNP) genotyping technologies suitable for large sample number and limited marker number, a microfluidic platform, namely Fluidigm 96.96 dynamic chip, was used to conduct the SNP genotyping system for identification of released individuals from stock enhancement projects. This study screened 96 high-quality polymorphic markers shared among salmonid species based on genotyping results of fish samples from 4 genera of Salmonidae using rainbow trout 57K SNP array. The microfluidic system was proved with high accuracy using Brachymystax lenok as testing populations, with a call rate of 98.63%, and the consistency with the previous Affymetrix 57K array reached 97.92%. Parentage assignments for 96 offspring individuals to their candidate parents and interfering parents were performed using CERVUS 3.0.7 software and the 96 SNP genotyping data. The results matched perfectly with the true pedigrees among complicated families, proving high accuracy in pedigree assignment application for the constructed microfluidic system. The non-exclusion probability for first parent (NE-1P) was 4.362×10^–4 during a single parent assignment, while the non-exclusion probability for parent pair (NE-PP) was as low as 6.538×10^–12. These results fully met the needs for molecular identification of released individuals, to determine if one captured fish was an offspring of documented broodstocks, which meant it’s hatched and released from certain stock enhancement projects. STRUCTURE analysis was also performed based on the 96 SNP genotyping data. The genetic components of 4 wild populations clearly distinguished, and the genetic composition of testing individuals were well demonstrated, suggesting that the constructed system is suitable for preliminary population genetic analysis for captured salmonid species. Thus, this study has great application potentials in fishery stock enhancement, to monitor the survival rate of released individuals, and to evaluate the supplemental effects on natural fishery resources.