Genetic variation was investigated in five subtidal locations from the north of San Matías Gulf (42°23′S) to the north of San Jorge Gulf (45°02′S). Fifteen loci were studied by means of vertical starch gel electrophoresis; ten loci were polymorphic. The percentages of polymorphic loci (P0·99 and P0·95 criteria) varied between 40% and 53·33% and between 33·33% and 46·67%, respectively. Expected mean heterozygosity per locus (He) ranged from 0·128 (Bajo Oliveira-El Sótano) to 0·160 (Puerto Madryn); this range is similar to those observed for other scallop species. All the loci were in Hardy–Weinberg equilibrium. The estimated genetic distances among populations were significantly lower than those reported for comparisons between populations of different pectinid species, suggesting that the five populations studied belong to the same species (Aequipecten tehuelchus). The absence of exclusive fixed alleles also supported that assumption. The results obtained suggest: (i) assignment of species or subspecies status to some morphological variants of the shells, like the ‘madrynensis’ form is not supported; (ii) the commercially exploited Tehuelche scallop from San Matías and San José Gulfs should be managed as distinct stocks.