The jumbo flying squid(Dosidicus gigas) is commercially important fishery species in the world.Assessment of population genetic diversity levels of jumbo flying squid is fundamental to the conservation and management of this species.The samples derived from the Chinese squid jigging vessel were collected from the eastern Pacific waters(81.9?-94.9?W,8.9?N-11.3?S)from July to October 2009.By using 724 bp fragment of mitochondrial cytochrome b gene(Cyt b),we analyzed the sequence variations and population genetic structures for 155 samples collected from seven sites of Peru and three sites of Costa Rica.In total,16 variable sites were acquired,and all of them were parsimony sites.43 haplotypes were identified from 155 individuals.Analysis of mtDNA Cyt b sequences of jumbo flying squids from the ten localities revealed that the mean haplotypic diversity was 0.873,while the nucleotide diversity was 0.003 69.6 haplotypes were shared by all the populations,while Peru population possessed the highest haplotypes(n=20).The AMOVA test of D.gigas revealed that 82.70% of the genetic variation occurred within populations.F_ST analysis suggested that significant genetic differentiations were found between the partial Peru populations and the Costa Rica populations,and even between partial Peru populations.However,no significant genetic differentiations were detected between Costa Rica populations.