Recent fieldwork and associated molecular and systematic studies on the bat fauna of the Comoro Archipelago (Grande Comore, Anjouan, Mohéli, and Mayotte) have provided new insights into the locally occurring species, their origins, and evolutionary history. Based on museum specimens, published studies, and our fieldwork, we provide a review of the Chiroptera of this archipelago. The Comoros, composed of in situ formed volcanic islands of recent geological age, occur midway between Madagascar and the African continent, and approximately 300 km of sea separate this island group from these two potential source areas for bat colonization. Ten species are documented in the Comoro Archipelago and the occurrence of one other species remains uncertain. Of these 10 taxa, one was new to science (Miniopterus aelleni) and two were new for the archipelago (Mops leucostigma and Chaerephon leucogaster), and all three of these taxa are shared with Madagascar. The only endemics to the Comoros are the fruit bats Pteropus livingstonii and Rousettus obliviosus, and the vespertilionid Myotis anjouanensis. Certain species occur on all four islands, while others have more limited distributions. Of the species known from the archipelago, five taxa or sister species occur on Madagascar, which appears to be the source of colonization, rather than the African continent. Based on current phylogeographic information, only one taxon, Miniopterus griveaudi, shows a clear pattern of genetic differentiation between different islands in the archipelago. Hence, in most cases a distance of 40–80 km separating the different islands does not form a measurable dispersal barrier to gene flow.