In order to resolve the population connectivity of skipjack (Katsuwonus pelamis) within the Indian Ocean, we analyzed thousands of genome-wide markers of individuals from a broad geographic area of the Indian Ocean, as well as from one location in the Atlantic Ocean. Our results support a complex stock structure with multiple genetically isolated populations co-occurring in most locations, and claim for additional analyses to further understand the population structure of skipjack tuna within the Indian Ocean.