Doryteuthis gahi is a small squid species that has a wide distribution in South America. This species is characterized by coastal and benthic spawning, and its ontogenetic vertical migration is associated with upwelling zones, features that may restrict its dispersal potential. It has also been proposed that populations of these neritic squid are structured by the influence of local processes which act as barriers to gene flow. Based on this background, we evaluate the geographical structure of genetic diversity in D. gahi along its distribution in the south-eastern Pacific Ocean. We used 116 COI mtDNA sequences of squid collected from different sites in Peru and Chile and calculated genetic diversity, the population structure index Fst, and performed analysis of spatial molecular variance and exact tests to detect differences among localities. To infer demographic history we carried out tests of neutrality and Bayesian skyline analysis. Although there was little molecular divergence between Peru and Chile, we detected a significant genetic differentiation of D. gahi along its geographical distribution. Squid from Chile showed higher genetic diversity than those of Peru and the results of the demographic inference analysis suggest that the population of Peru is experiencing or experienced in the recent past demographic expansion, a pattern that was not found in Chile. We think that the current genetic patterns are consequences of northward migrations in the glaciation periods and posterior re-colonization of southern Chile in the deglacial period. Copyright © 2011 Marine Biological Association of the United Kingdom.