Abstract: During the exploitation of purpleback flying squid Sthenoteuthis oualaniensis resources in the northwestern Indian Ocean (13°N~20°N, 59°E~64°E) from September to December in 2004 and from March to May in 2005, 48 individuals muscle samples collected from 12 stations were used for population genetic structure identification by Random Amplified Polymorphic DNA (RAPD) analysis. The results showed that the purpleback flying squid in the northwestern Indian Ocean could be divided into two populations by UPGMA clustering analysis.One population distributed in the area of 13°N~18°N, while another population distributed in the area of 18°N~20°N. The results showed that high genetic variations were found within population and the coefficient of genetic differentiation between the two populations was 0.2150, which indicated that quite different genetic background existed in the two populations. Shannon′s diversity index was 0.3676±0.1801. Genetic distance between the two populations was 0.1338, and genetic similarity was 0.8748.