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Eleginops maclovinus, the Patagonian blennie, is a notothenioid (Perciformes) endemic to South American temperate and sub-Antarctic waters. Here, we report ten polymorphic microsatellite loci isolated from a dinucleotide-enriched E. maclovinus genomic library. Among 48 individuals, the number of alleles per locus ranged from eight to 41, and the observed and expected heterozygosity ranged from 0.688 to 0.938 and from 0.695 to 0.968, respectively. No locus significantly deviated from HardyWeinberg equilibrium, and no significant linkage disequilibrium between pairs of loci was found. These polymorphic microsatellite loci will be useful for investigating genetic population structure and connectivity among natural populations.