These hypotheses have proposed the occurrence of two subspecies in the South-eastern Pacific (Merluccius gayi gayi and Merluccius gayi peruanus), however there are not sufficient evidences that support such hypotheses. In this work the genetic differences between the subspecies is analyzed using protein electrophoresis. Twenty-five individual of M. gayi gaq'i from Talcahuano (Chile) and the same number of M. gayi peruanus from the Port of Paita (Peru) were analyzed. It was detected the genic product of 33 loci homologous. The taxa showed a differential mobility in the monomorphic loci EM-2*, AP-1* and AC-1* and the polymorphic locus EST-3*. Merluccius gayi gayi exhibited a greater variability when compared to M. g. peruanus (24% of polymorphism and 0.075 mean heterozygosity waited for M. g. gayi and 18% of polymorphism and 0.042 mean heterozygosity waited for M. g, peruanus). The genetic identity among the taxa was 0.873, with an estimated separation time between 900,000 to 2,000,000 years (Pleistocene). The relationships between both taxa were analyzed in light of the historical biogeographical events.