The chokka squid, Loligo reynaudii, is the target of a commercially valuable fishery in South Africa, but little information is available on population structure and mating system. We developed 11 polymorphic microsatellite markers using both standard nonenrichment and enrichment protocols. Numbers of alleles per locus ranged from 11 to 30, and levels of expected heterozygosity ranged between 0.77 and 0.98. Three loci developed using an enriched library displayed significant departure from Hardy–Weinberg genotype proportions suggesting high frequencies of null alleles. The remaining loci should prove useful for population and parentage studies.