The population structure of the jumbo squid (Dosidicus gigas) is complex, containing several cohorts and three groups defined by their size (small, medium, and large) and by differences in maturation, growth, and life span. Several authors have indicated the possibility of such groups representing discrete genetic units even at level subspecies or species in statu nascendi. Genetic divergence was tested in samples from the Gulf of California (Mexico) and Peruvian Sea by estimation of population divergence statistics, an exact test of homogeneity of allele frequencies, analysis of molecular variance, and genealogical trees applied to data obtained with two molecular markers: RAPDs and mtDNA sequences identified by SSCPs. Neither significant values of θ (FST) nor significant heterogeneity in allele frequencies were detected. Lack of evidence does not imply complete lack of differentiation among the groups but supports the fact that a geographically spread population can have different size groups without relevant genetic differentiation, implying that the hypothetical genetically differentiated groups can occur in different ecological niches.