According to the IUCN global Red List, Pipistrellus maderensis is among the most endangered bat species in Europe. Its populations are scattered across some islands of the Atlantic Ocean, particularly Madeira and the Canary archipelagoes. This geographical pattern is likely to result in significant genetic differences between populations which would have important implications to set conservation priorities. To test this hypothesis, we analyze cytochrome b sequences and compared populations from Madeira and the Canary islands. Five sequences from Madeiran individuals were analysed and compared to 30 sequences extracted from GenBank from Pipistrellus maderensis from the Canary islands and Pipistrellus kuhli.

Our results indicate a significant divergence between the two groups, smaller than between true species, but higher that intra-group divergence. However, further research on the Madeiran population is needed, including the use of sequences of other mitochondrial markers and nuclear marker and microsatellites.