Infection patterns of trophically transmitted helminth parasites were compared with feeding ecology in two sympatric whitefish Coregonus lavaretus morphs from two lake systems in northern Norway. In both lakes, the pelagic morph was an obligate zooplanktivore, while the benthic morph utilized both the benthivore and zooplanktivore trophic niches. The differences in niche utilization between the two morphs were associated with differences in trophic morphology (gill raker numbers), suggesting that they were genetically dissimilar and reproductively isolated. The benthic morph had the highest number of helminth species, probably because they exhibited a broader niche width compared to the pelagic morph. In both lakes, the species composition and intensities of helminths reflected the trophic diversification of the whitefish ecotypes with respect to different habitat choice (benthic v. pelagic) and dietary specialization (benthivore v. zooplanktivore feeding strategies within the benthic whitefish morph). Zooplanktivorous fish from both morphs acquired parasites mainly from pelagic copepods and in almost equal quantities. The benthivore feeders within the benthic morph had the highest proportion of parasites with transmission stages from benthic organisms. Host feeding behaviour seemed to be a major determinant of the helminth community structure, and helminths appeared to be useful indicators of long-term trophic specialization of whitefish ecotypes.