The population genetic structure of three rare and declining bumblebee species, Bombus muscorum, B. humilis, and B. sylvarum was examined using microsatellite markers. We find evidence of significant genetic structuring in both oceanic island populations of B. muscorum and in fragmented mainland populations of B. jumilis and B. Sylvarum. In the former species we find that all populations greater than 10km apart are significantly differentiated from one another suggesting dispersal above this distance is infrequent. Evidence of genetic bottlenecks was found in populations of both B. muscorum and B. humilis. All three species show reduced genetic diversity relative to the common B. pascuorum and fragmented UK populations of B. sylvarum show reduced genetic diversity relative to a continental population. Effective population sizes were found to be low in B. humilis and B. sylvarum, especially so in the latter species. Diploid male production was observed in all three rare species, but was infrequent. We propose that diploid male production is not an appropriate measure of inbreeding depression for social Hymenoptera. Why some bumblebee species have declined in the face of agricultural intensification while others have not is not well understood. Diet breadth of rare species was examined as a possible explanation of this. To some extent all three rare species studied show a narrow diet breadth. We hypothesize that this is because as these species emerge late, they must specialize on plants with higher quality pollen in order to raise the brood more quickly. Following losses of floral diversity, agricultural intensification has than affected these species more greatly.