In this study, we determined the mitochondrial DNA cytochrome b gene (Cytb) sequences of the northern, equatorial and southern populations of Sthenoteuthis oualaniensis in the Eastern Indian Ocean, and analyzed the phylogenetic relationship.It was shown that S. oualaniensis in the Eastern Indian Ocean had an overall high haplotype diversity of 0.939 and a high nucleotide diversity of 0.015.F_st value among three populations was 0.661 (P<0.01), reaching a high level of interpopulation genetic differentiation with significant genetic structure. Two lineages were revealed in three S. oualaniensis populations in the Eastern Indian Ocean. Lineage 1(the northern lineage of the Eastern Indian Ocean) is dominated by individuals from the northern population of the Eastern Indian Ocean; lineage 2(the southern lineage of the Eastern Indian Ocean)mainly consists of individuals from the equatorial population and the southern population of the Eastern Indian Ocean,and lineage 2 underwent population expansion. The great north-south hydro-logical difference in the Eastern Indian Ocean may be the reason for the north-south lineage divergence of S. oualaniensis in the Eastern Indian Ocean. The differences and characteristics of the north-south lineages should be considered in the utilization and management of S. oualaniensis resources in the Eastern Indian Ocean.