Spatial genetic structure in the highly migratory striped marlin (Kajikia audax) was examined using nuclear (microsatellite) and mitochondrial (control region sequences) DNA markers. While previous studies on striped marlin were limited by sampling design and sample size, this study employed a multiyear concurrent sampling scheme to collect tissue from seven locations representative of the species’ range in the Pacific: Japan, Hawaii, Southern California, Mexico, Central America, New Zealand, and Australia. Mature and immature specimens were analyzed separately to evaluate life-stage-specific population structure and movements. Microsatellite and sequence results revealed small but significant overall spatial subdivision (F_ST = 0.0145 and K_ST = 0.06995, respectively). Pairwise microsatellite analyses (n = 1199) revealed four groups: (1) Japan – Immature Hawaii – Southern California, (2) Mature Hawaii, (3) Mexico – Central America, and (4) Australia – New Zealand. Mitochondrial sequence analysis (n = 451) showed similar patterns; however, no significant differentiation was found between groups 1 and 2. This enhanced resolution of geographic genetic structure is important for understanding the complex migration patterns in this species. Moreover, the consistency among independent genetic studies on striped marlin provides strong support for management of at least three clearly delineated Pacific stocks.