Bacteria play an important role in the nutrition of many lake-dwelling detritivorous macroinvertebrates, yet few studies have investigated the roles of differing groups of bacteria in freshwater systems. Recent stable carbon isotope analyses have revealed that methanotrophic bacteria help fuel lake food webs. We analysed individual larvae of co-existing Chironomus plumosus and C. anthracinus for stable sulphur isotopes as an alternative tracer for bacterial assimilation, and compared them with existing stable carbon isotope data. The combination of these 2 isotopes suggests that there are large inter- and intraspecific differences in the incorporation of bacteria rather than algae in the diet of both species. C. anthracinus appears to assimilate a greater proportion of chemoautotrophs relative to its congener, which is consistent with classical descriptions of C. anthracinus feeding mode relative to bacterial stratigraphy in the sediments. The higher intraspecific isotope variability of C. plumosus indicates variable proportions of methanotrophs, chemoautotrophs and phytoplankton to the diets of individuals.