The migratory tunas (scombrid species) are of paramount importance for the international seafood trade. In order to ensure a sustainable use of these multi-stake holder fisheries resources, it is crucial that stock delineation and management plans are in accordance. Here, we examined the population genetic structure of wahoo (Acanthocybium solandri) and bigeye tuna (Thunnus obesus), two key species of growing significance in tuna fisheries. Our study employed whole-genome sequencing methods to conduct the most extensive genomic analysis of wahoo and bigeye tuna samples to date, collected from the Atlantic, Indian and Pacific Oceans. This ENA study project contains the sequencing data for bigeye tuna.