Mosses provide habitat for microarthropod communities that are dominated in abundance and richness by mites. Although these systems are used as experimental models to address questions of relevance to general ecology, and despite the fact that they are also of relevance to key, ecosystem-wide functions such as nutrient cycling rates, the trophic relationships that underpin these functions are poorly resolved. The complexity of the moss habitat matrix and the small size of its residents have hampered progress in the determination of diets. We use stable isotope analysis of moss communities and present tools that allow for more in-depth studies of food web structure in mosses and soils than are currently available. We test in mites for the first time the association between mouthpart morphology and isotope signatures. Isotopes capture the diet of mites under field conditions and over a longer time-span than traditional, snapshot measures of diet such as gut contents analyses. Our data suggest that cheliceral morphology can be used as a first inexpensive and quick filter for estimation of dietary preference in mites, with ambiguous trophic relationships resolved through isotope analyses. This work provides new information and tools for the study of mite-dominated food webs.