Swordfish (Xiphias gladius) is of significant economic importance as it is the second most exploited billfish in the Indian Ocean. While the Indian Ocean Tuna Commission (IOTC) considers swordfish to be a single panmictic population in the Indian Ocean, several studies have examined the potential for spatial variations within this highly migratory species with conflicting results, including emerging evidence that population structuring does indeed exist within swordfish. These findings therefore raise questions about the current guidelines for management adopted by the IOTC. In the present study, we address questions about the genetic structuring of swordfish in the Indian Ocean through the analysis of three datasets: (i) neutral SNPs, (ii) with, and (iii) only SNPs under potential selection identified from 1694 swordfish originating from 24 distinct locations across the Indian Ocean. A discriminant analysis of principal components showed the presence of two swordfish subpopulations in the Indian Ocean in the north and the south and was confirmed by admixture methods. This genetic differentiation may be explained by a chromosomal inversion, indicating that both populations could be demographically connected but remain differentiated by this structural variant.