This study reports the distribution of parasite genotypes for the trypanosome Crithidia bombi across individual units (the colonies) in host populations of a social insect, the bumble bee Bombus terrestris. A number of microsatellite primers were developed and several of them were found to be polymorphic in our samples. Furthermore, a simple algorithm was used to identify the likely multi-locus genotypes present in multiply infected host individuals. The results demonstrated a remarkably high degree of genetic diversity among infections. A first sample from 1997 could only use a low resolution with 2 loci and showed a total of 11 different genotypes of C. bombi from 12 colonies. The sample from 2000 was analysed at 6 polymorphic loci and contained data from 8 colonies that were infected by 27 different C. bombi genotypes. Roughly 16% of all individual bees but half of all colonies (2000 sample) were infected with more than 1 genotype. The infections in the different colonies were also genetically distinct from each other, and the parasite population as a whole was in linkage disequilibrium and deviated from Hardy-Weinberg expectations. The highly structured and genetically diversified population of C. bombi is likely to result from strong genotypic host-parasite interactions.