The purpleback flying squid (Sthenoteuthis oualaniensis) is a pelagic squid with tremendous potential for commercial exploitation. We isolated and characterized 21 polymorphic microsatellite loci for S. oualaniensis using a (GT)13-enriched genomic library. The number of alleles per locus varied from 6 to 32. The observed and expected heterozygosities ranged from 0.188 to 0.890, and 0.537 to 0.968, respectively. No significant linkage disequilibrium was detected at these loci.