Cunninghamella echinulata var. elegans is a model system for the study of metabolism of toxic compounds. Unlike most other zygomycete fungi, Cunninghamella can use nitrate as a sole N source. We generated nitrate-nonutilizing (Nit(-)) mutants in three isolates of C. echinulata var. elegans. Mutants at the niaD and nirA(-) loci were unable to complement each other, suggesting that this fungus is vegetatively self-incompatible. Vegetative self-incompatibility may prove advantageous for using Cunninghamella for in situ bioremediation.