Genetic variability within colonies of eusocial insects is often higher than expected if kin selection alone explains sociality. Parasites and pathogens have been proposed as selective agents maintaining genetic variability in populations and promoting polyandry in social insects. Using the natural system, bumble bees, Bombus terrestris, and their trypanosome parasites, Crithidia bombi, we find that hosts vary in susceptibility or parasites in infectiousness, and that parasite transmission in social groups correlates with genetic relatedness among hosts. Therefore parasite-mediated negative frequency-dependent selection could play an important role in structuring the genetic composition of social groups by counteracting kin selection for high relatedness.