Abstract: In this study SLAF-seq technique based on the next generation sequencing platform was used to develop Decapterus maruadsi microsatellite markers. Ninety-three microsatellite loci were randomly selected from 1 450 multiple nucleotides microsatellite loci with tetra-nucleotide to hexa-nucleotide bases for primer synthesis and polymorphism detection. Finally, thirty-one highly polymorphic markers were developed. The population genetic analysis resulted a high polymorphism with a range of 4 to 29 alleles (mean 13.48). Observed and expected heterozygosities varied from 0.281 to 0.875 (mean 0.650) and 0.557 to 0.958 (mean 0.838), respectively. The average of polymorphism information content was 0.803 (ranged from 0.456 to 0.939) indicating that the 31 microsatellite markers were highly polymorphic. The results of Hardy-Weinberg equilibrium test showed that 17 microsatellite markers conformed to HWE, and no chain imbalance was detected. Cross-amplifications discovered a total of 27, 20, 20, 18, and 9 out of 31 microsatellite markers were successfully across in Decapterus macarellus, Decapterus macrosoma, Decapterus kurroides, Trachurus japonicus and Selaroides leptolepis, respectively. These long repeat microsatellites can provide a powerful genetic tool for assessment of scientific management and conservation of the blue scad fishery resources. In addition, it provides a new tool in studying phylogenetic relationship among the Decapterus and Carangidae species.