Habitat loss has led to fragmentation of populations of many invertebrates, but social hymenopterans may be particularly sensitive to habitat fragmentation due to their low effective population sizes. The impacts of fragmentation depend strongly on dispersal abilities, but these are difficult to quantify. Here, we quantify and compare dispersal abilities of two bumblebee species, Bombus muscorum and Bombus jonellus, in a model island system. We use microsatellites to investigate population genetic structuring, dispersal and spatial patterns in genetic diversity. Populations of both species showed significant structuring, and isolation by distance, but this was markedly greater in B. muscorum (θ = 0.13) than in B. jonellus (θ = 0.034). This difference could reflect a higher effective population size in B. jonellus compared to B. muscorum, but this is not consistent with the observed abundance of the two species. We argue that it is more likely that B. jonellus has a higher propensity to disperse than B. muscorum. This will influence their relative susceptibility to habitat fragmentation and may in part explain differential declines of mainland populations of these and other bumblebee species.