Abstract The sailfish (Istiophorus platypterus) is a mobile epipelagic billfish whose range extends across the world’s tropical and subtropical oceans. Once thought to be two allopatric species, respectively inhabiting the Indo-Pacific and Atlantic oceans, molecular analyses support a single species with global distribution. Adequate sampling of widespread pelagic species presents considerable challenges, and most previous studies on sailfish used small numbers of molecular markers. As such, our understanding of their global population structure was limited. In this study, we collaborated with fisheries researchers and fishers to build a comprehensive genomic dataset of single-nucleotide polymorphisms for sailfish spanning most of its range. Here, we examined genetic variation using three filtering approaches: (i) the full-loci dataset, (ii) putatively neutral loci, and (iii) large-FST loci for 590 sailfish from 20 locations to explore contemporary population structure and connectivity in a global context. Cluster analyses of all datasets indicated three discrete populations: the Atlantic, eastern Pacific, and Indo-West Pacific oceans. For the first time, sailfish sampled from locations across the Indo-West Pacific revealed genetic connectivity throughout this region. Analyses of a subset of large-FST loci suggested a small reduction in gene flow between the western and eastern Atlantic Ocean and between the western Indian Ocean and the rest of the Indo-West Pacific. These insights into contemporary population structure can inform future stock assessments and cross-jurisdictional management of this migratory marine species.