Stable isotope analyses of chironomid trophic interactions have recently indicated the potential importance of isotopically light biogenic methane as a carbon source. Mass balance of isotope ratios suggests that small proportional differences in ingestion of such an isotopically distinct basal resource by individual consumers can result in considerable intraspecific variability. To test this, we collected individual larvae of two closely related chironomid species (Chironomus anthracinus and Chironomus plumosus) from six lakes and analyzed their delta(13)C and delta(15)N. Intraspecific variability in larval delta(13)C and delta(15)N values was greater in lakes where chironomids were more C-13 depleted. C plumosus exhibited higher intraspecific variability relative to C anthracinus. In two lakes, individual C. plumosus exhibited a range of 35parts per thousand for delta(13)C and 16% for delta(13) N (equivalent to five trophic levels). There was a strong positive relationship between larval delta(13)C and delta(15)N, both between individuals from the same lake and also between lakes, suggesting that the underlying causative mechanisms are similar. Furthermore, larvae from deeper sites, which are more susceptible to prolonged anoxia, exhibited greater intraspecific variability, and larger larvae were significantly C-13 depleted. Such high intraspecific variability can confound the interpretation of benthic food web stable isotope values. We advocate the reporting of more intraspecific isotopic variability as a means to further examine niche breadth and feeding behavior.