Abstract: To understand the genetic differentiation and structure among the large, medium and small phenotypic groups of Dosidicus gigas in the Southeast Pacific Ocean, we studied a total of 90 samples of matured D. gigas from different phenotypic groups for population genetics by using the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. The average haplotype diversities (H_d) and nucleotide diversities (P_i) of the three groups of D. gigas were 0. 818 and 0.002 40, respectively, showing a high haplotype diversity index but a low nucleotide diversity index. The genetic variation observed within populations reached 100.45%. The value of genetic differentiation index (F_st) was less than 0.05 (P>0.05), but the gene flow (N_m) was far more than 1, indicating no significant genetic divergence among the three phenotypes of D. gigas. The neutrality test was highly significantly negative (F_s=−8.617 73, P<0.01) and the nucleotide mismatch distribution curves all showed significant single peaks, suggesting that D. gigas in the Southeast Pacific Ocean might have historically experienced rapid population expansion events. In conclusion, there may be extensive genetic exchange between different phenotypic groups of D. gigas in Southeast Pacific Ocean due to their reproductive behavior and that they should belong to the same stock, which must be fully considered in fisheries management.