Longtail tuna (Thunnus tonggol), kawakawa (Euthynnus affinis) and narrow-barred Spanish mackerel (Scomberomorus commerson) are important fish resources in the Indian Ocean. These species are currently managed as single stocks. Studies to date have not demonstrated strong evidence of population structure. In this study we report results from the multi-agency, collaborative PSTBS-IO project, which involved large-scale sampling and cutting-edge sequencing technology to investigate the genetic population structure of these three neritic species, along with priority tropical and temperate tuna, billfish and sharks. These analyses provide strong evidence of at least three, two and four different populations in the Indian Ocean for longtail tuna, kawakawa and the narrow-barred Spanish mackerel respectively. These results warrant re-consideration of how these species are monitored and managed in the Indian Ocean and highlight the need for further targeted research to confirm the temporal stability of these results and provide a comprehensive understanding of population boundaries for these species within the Indian Ocean.