The chemical composition of fatty acids and ubiquinones was studied in 18 strains of Cunninghamella, to establish quantitative and qualitative differences within the genus. Fatty acids analysis has shown the presence of four groups. Ubiquinone analysis, through high performance liquid chromatography (HPLC), demonstrated the existence of three different groups based on the ubiquinone type. The average percentage of fatty acids of the species Cunninghamella elegans and Cunninghamella bertholletiae, show variations in linolenic and stearic acids, suggesting the possibility of differentiation between the two species.