Jumbo squid, Dosidicus gigas, is commercially important species in the Eastern Pacific Ocean, principally in the Northern Humboldt Current System where is notably abundant. In this area, jumbo squid display difference in density at geographical level, in size of mature individuals and inter-annual demographic fluctuation. Thereby, a population genetics study of jumbo squid in this location is needed especially for fisheries management. This study evaluated the population genetic of this squid (n = 120) based on novel microsatellite loci and 675. bp of the mtDNA ND2 divided into two groups according to the Geographical density and Size at maturity. Our results at nuclear loci showed an overall low genetic diversity and no signatures of genetic differentiation of any group. At mtDNA loci level, low but significant genetic differentiation were detected between Small (n = 33) and Large (n = 39) populations. The low genetic diversity is more likely explained by a historical demographic expansion whereas the contradictory results of population structure may be due to the low number of microsatellite loci in HWE, different maternal history of this species or the different influence of genetic drift on mitochondrial and nuclear genes. Furthermore, demographic history analysis suggested that jumbo squid population went through a period of pure demographic expansion over the last 50,000 years ago. This study provides results of combined nuclear and mtDNA molecular markers that was never reported before and may represent a valuable information for the monitoring of the population genetic of this species.