We investigate the genetic relationships between purported island species of Pteropus fruit bat (Megachiroptera) from the western Indian Ocean islands using mitochondrial DNA sequencing in order to infer the pattern of colonisation of this biogeographic region. Most significantly, our genetic data questions the current taxonomic assignment based on morphology of many of the island species and subspecies, suggesting instead that many of the western Indian Ocean islands harbour 'races' of P. giganteus from mainland India. Our results strongly argue against a single colonisation event from mainland Asia. Evidence is presented for three colonisation events; the first to the western-most extremity of their range (Comoros and Pemba Island), the second to Rodrigues Island; and a third giving rise to the remaining extant island taxa, the latter two events occurring relatively recently and rapidly.