The ecological theory of adaptive radiation states that differences in ecological circumstances among local populations are the cause of divergence that leads to speciation. The role of parasites in contributing to divergence has seldom been considered, despite their ubiquity and known selective effects. The potential for parasites to contribute to divergence between closely related taxa was examined by quantifying the variation in parasite burdens between sympatric three-spined stickleback species (Gasterosteus aculeatus complex) in two lakes in coastal British Columbia, Canada. In doing so the relative importance of geographical differences between lakes and trophic or microhabitat differences between species within lakes were evaluated. The entire metazoan parasite burdens of a total of 255 limnetic and benthic sticklebacks in Paxton and Priest lakes were assayed over five time points between spring and autumn. Despite their sympatric distributions, there were large differences in parasite burdens between benthic and limnetic sticklebacks within lakes and these were consistent across both lakes. In particular, limnetics suffered greater burdens of the parasites Schistocephalus solidus and Diplostomum scudderi and benthics had much higher burdens of parasitic glochidia (mollusc larvae). Parasite burdens also differed quantitatively between lakes, but in general such differences were less pronounced than those between the stickleback species. The documented differences in parasite burdens between stickleback species have potential to contribute to divergent selection on life history, immunological and secondary sexual characters that could contribute to reproductive isolation between the species.