The Mauritius flying fox Pteropus niger is distributed on the islands of Mauritius and La Réunion in the western Indian Ocean. Although recent studies have examined the phylogenetics and systematics of this genus, relatively few have assessed the population genetics of species distributed on oceanic islands and no study has focused on the demographics of P. niger. Here, we present mitochondrial DNA sequence data from 39 individuals of P. niger collected from four main colonies distributed throughout Mauritius. Our results indicate that the Mauritian population of P. niger is likely panmictic, with moderate to high levels of gene flow occurring among colonies distributed across the island. Collectively, our sequence data suggest moderate levels of genetic variation within the population. These findings will help to inform ongoing conservation and disease surveillance initiatives.