During the late Pleistocene-Holocene, the Humboldt Current System (HCS, Peru-Chile) was subject to important oceanographic variations that may have affected the abundance and distribution of marine populations, as well as their genetic structure and diversity. The fast growth and short life span of jumbo squid Dosidicus gigas make this squid a valuable model organism for evaluating how environmental fluctuations affect the genetic diversity of marine populations. We sequenced a 657 bp fragment of the mtDNA cytochrome c oxidase I (COI) gene of 169 jumbo squids from 6 locations in the HCS. We measured and compared genetic diversity among localities and performed neutrality tests to detect deviation from mutation-drift equilibrium. We inferred the demographic history of jumbo squids using Bayesian skyline analyses to estimate effective population size through time. A total of 23 haplotypes were found among the sequences. Haplotype and nucleotide diversity were low in all locations. D. gigas was characterized by an absence of population genetic structure and a star-like haplotype network. Neutrality test values were negative and statistically significant, and therefore consistent with a past population expansion. Similarly, Bayesian skyline analyses indicated a recent demographic expansion after the last glacial maximum. Our results suggest that D. gigas consists of a single, large population in the HCS, that may have experienced a dramatic demographic popu lation expansion consistent with the oceanographic changes associated with the last glacial- interglacial transition. © Inter-Research 2011.