The bumble bee Bombus terrestris L. is a geographically variable species with a wide distribution in Europe, the near East, northern Africa, Mediterranean islands, the Canary Islands and Madeira. Based on morphological and coat colour pattern differences, the bumble bee populations of the Canary Islands and Madeira are currently treated as separate species, B. canariensis and B. maderensis, respectively. To analyse the phylogeographical associations of these bees with continental B. terrestris, one population each from four islands of the Canaries and one population from Madeira were studied. Genetic variability was assessed at nine microsatellite loci and a fragment of the mitochondrial gene cytochrome b. Genetic differentiation among islands, and between islands and the continent, was extensive. A NJ-tree based on microsatellites strongly supported the distinctness of the Canary Island populations, whereas the Madeira sample was genetically more similar to the continental populations of B. terrestris from Europe. MtDNA sequence data were in good agreement with nuclear markers. They suggest that haplotypes ancestral with respect to B. lucorum occur on the Canary Islands, whereas derived haplotypes were found on the European continent. The Madeira population shares the most common haplotype of continental B. terrestris. Nuclear and mtDNA data both indicate that bumble bees from the Canaries and Madeira do not share a common colonization history.