Nine novel microsatellite loci were developed for Trachurus murphyi. These loci were characterized in samples from three sites along the eastern South Pacific Ocean. One of the loci was monomorphic, whereas the rest of the loci had between six and 19 alleles per locus and showed the expected heterozygosity ranging from 0.653 to 0.933. These loci do not show genetic differentiation among the analyzed sites.