Understanding population connectivity in highly migratory pelagic fishes is essential for effective fisheries management. We investigated population structure in swordfish (Xiphias gladius) using genome-wide single nucleotide polymorphism (SNP) data from individuals collected across 12 regions spanning across the Pacific and Indian Oceans. Population structure was assessed using multiple complementary approaches, including principal component analysis (PCA), genetic differentiation statistics, analysis of molecular variance (AMOVA), and clustering analyses. Overall genetic differentiation among regions was low, indicating high levels of connectivity and gene flow across the study area. However, all analytical approaches detected significant population structure. The strongest differentiation was observed between samples from the northern Indian Ocean and the remaining regions. In contrast, samples from New Zealand, Norfolk Ridge, the East Tasman Basin, and adjacent Tasman Sea regions showed substantial overlap in ordination and clustering analyses, with little evidence of genetic divergence. These findings indicate that Indo-Pacific swordfish comprise a highly connected genetic system with weak but detectable population structure. The observed pattern is consistent with broad north-south structuring within the Indian Ocean, rather than complete panmixia, and may reflect regional differences in spawning dynamics, movement patterns, or oceanographic processes influencing connectivity. This study provides an important genomic baseline for evaluating stock boundaries and improving fisheries assessment and management throughout the Indo-Pacific.