Pollicipes elegans is a commercially important and biogeographically significant rocky-shore gooseneck barnacle found along the eastern Pacific coasts of Peru, El Salvador, and Mexico. Little is known about its reproductive biology, and no genetic resources exist despite its growing importance as a fisheries species in the region. Next generation sequencing methods can provide rapid and cost-effective development of molecular markers such as microsatellites, which can be applied to studies of paternity, parentage, and population structure in this understudied species. Here, we used Roche 454 pyrosequencing to develop microsatellite markers in P. elegans and made genomic comparisons of repeat density and repeat class frequency with other arthropods and more distantly related taxa. We identified 13 809 repeats of 1–6bp, or a density of 9744bp of repeat per megabase queried, which was intermediate in the range of taxonomic groups compared. Comparison of repeat class frequency distributions revealed that P. elegans was most similar to Drosophila melanogaster rather than the more closely related crustacean Daphnia pulex. We successfully isolated 15 polymorphic markers with an average of 9.4 alleles per locus and average observed and expected heterozygosities of 0.501 and 0.597, respectively. Four loci were found to be out of Hardy–Weinberg equilibrium, likely due to the presence of null alleles. A preliminary population genetic analysis revealed low but significant differentiation between a Peruvian (n = 47) and Mexican (n = 48) population (F ST = 0.039) and markedly reduced genetic diversity in Peru. These markers should facilitate future studies of paternity, parentage, and population structure in this species.