The cordonnier Siganus sutor is a marine fish that inhabits the estuaries, rock reefs, and the inner pavement areas of coral-reef flats of the Western Indian Ocean (WIO). We investigated the genetic structure of the cordonnier using nuclear and mitochondrial markers from seven localities in the WIO. Based on their geographic distribution, we identified two genetically distinct ensembles, one in the Mozambique Channel (MZC) and one in the Mascarene Islands (MAS). Bayesian structure assignment showed little admixture, leading us to suspect that the cordonnier may alternatively consist of two species. Under the latter hypothesis, the weak gene flow would correspond to occasional hybridization, also offering an alternative explanation for asymmetrical gene flow at the mitochondrial locus.