Biological soil crusts of the arid Southwest US are habitat for a greater diversity of microfauna than soils with absent or physically disturbed crusts. The cyanobacteria of desert soil crusts fix nitrogen biologically, but it is not known whether these cyanobacteria are consumed by microfauna and are a significant component of the soil food web. We suspect that stylet-bearing nematodes and tardigrades are the most likely microfauna to graze on cyanobacteria, so we used natural abundance stable isotopes to test whether cyanobacteria are indeed a significant component of their diet in the field. We found that stable isotope composition of microinvertebrate biomass supports the hypothesis that cyanobacteria are a potential prey item in the food chain leading up to tardigrades and dorylaim-type nematodes in desert soils, but does not support the same hypothesis for Tylenchidae in these communities. Continued development of stable isotope methods may help to refine our understanding of feeding behaviors in belowground desert soil food webs.