The saprotrophic fungus Fusarium culmorum, Penicillium hordei, Rhizoctonia solani and Trichoderma harzianum and the arbuscular mycorrhizal fungus Glomus intraradices were examined for content of phospholipid fatty acids (PLFA) and neutral lipid fatty acids (NLFA). The AM fungus differed from the saprotrophic fungi especially by its content of the fatty acid 16[ratio ]1ω5 which was absent in the saprotrophs. The fatty acid 18[ratio ]2ω6,9 was the dominant fatty acid of the saprotrophic fungi while it was negligible in mycelium of G. intraradices. Specificity in content of fatty acids made it possible to quantify G. intraradices and F. culmorum simultaneously in soil. Furthermore, a compartmented growth system made it possible to study mycelial interactions in the absence of roots. We measured hyphal spread of both fungi, hyphal 33P transport of G. intraradices and sporulation of F. culmorum. The two fungi did not interact according to the parameters used in this study. We conclude that fatty acid signatures may be a valuable tool when studying interactions between AM fungi and other fungi in root-free soil.