Abstract: A total of 58 180 microsatellites were developed by RAD-Seq high-throughput sequencing technology in Decapterus macrosoma. One hundred and twelve microsatellite loci were randomly selected from di-/tri-nucleotide repeat microsatellite loci. Finally, twenty-seven highly polymorphic markers were developed. The population genetic analysis finds 18 dinucleotide-repeated microsatellite loci (9−14 repeated) and 9 trinucleotide-repeated microsatellite loci (6−10 repeated). The number of alleles (N_a) ranged from 5 to 17 (mean 10.6). The observed and expected heterozygosities ranged from 0.342 9 to 0.857 1 (mean 0.631 7) and 0.538 3 to 0.911 8 (mean 0.796 8), respectively. The polymorphism information content (PIC) ranged from 0.497 to 0.886 (mean 0.780 9), and the PIC at all loci except for one was geater than 0.500, indicating that the microsatellites were highly polymorphic. The Hardy-Weinberg equilibrium (HWE) test shows that 19 microsatellite markers conformed to HWE. There is no linkage imbalance among the 27 loci. The 27 microsatellites developed by this study will be useful for further population genetic analysis.