Host density, genetic diversity and social structure are key factors influencing disease transmission in wildlife populations, but their interactions remain poorly understood in insects. We assessed how populations of two common bumble bee species, Bombus pascuorum and B. terrestris are structured across island and mainland sites in the British Isles and France. B. pascuorum formed distinct genetic clusters on islands, with varying levels of heterozygosity with only the Isle of Arran in Scotland clustering with mainland populations. B. terrestris populations were less structured, indicating a higher dispersal ability; however, populations on the Isle of Man and the Scilly Isles showed low heterozygosity, and the Isle of Man was genetically separated from other islands and mainland populations. Nest density was similar between species. To assess how population structure affects pathogen prevalence, we tested bees for five micro-parasitic and four viral pathogens, expecting higher pathogen transmission within nests and in dense, genetically homogenous populations. B. pascuorum from the same nest showed more similar infection profiles than bees from different nests, indicating increased intra-colony transmission. Contrary to expectations, islands with high heterozygosity showed high viral prevalence and no reduction in micro-parasite infections. Bumble bee nest density was linked to a higher prevalence of Apicystis bombi, while other pathogens showed inconsistent patterns. These results suggest that while social structure affects pathogen transmission, genetic diversity does not consistently reduce prevalence. Instead, generalist bumble bee pathogens could be more affected by host species diversity and density. Island populations with limited gene flow and low genetic diversity may be more vulnerable to pathogen pressure, particularly under changing environmental conditions.