Stock structure of swordfish (Xiphias gladius Linnaeus, 1758) from four areas of the South West Indian Ocean was conducted using Restriction Fragment Length Polymorphism (RFLP) on mtDNA control region and six amplified microsatellite loci. No significant differences were found among the four locations using either molecular technique. Most variability was found within populations, with only a small proportion of variation among samples, suggesting a unique stock of swordfish in the South West Indian Ocean. The sample size of this study is too small to reveal significant structure among the sampling locations. These results are baseline for a future larger scale project in the whole Indian Ocean.