The coastal pelagic fish Normanichthys crockeri inhabits the southeast Pacific coast and is a monotypic species of the Normanichthyidae family. Its ecologically and economic importance, and the high fishing pressure it is subjected to make N. crockeri an ideal target species for conservation. Here, we present 12 new hypervariable loci for this species. Allelic richness varied between 2 and 8 alleles, and observed heterozygosity ranged between 0.059 and 1.00. Two loci showed significant deviations from Hardy–Weinberg and revealed the presence of null alleles. These new loci have a high potential to be used in population genetics studies and fishery management plans.