AbstractMycorrhizal fungi are usually identified on the basis of the morphological characters shown by fruit bodies, spores, vegetative mycelia or symbiotic structures. The development of molecular techniques provides a valuable and alternative approach to identify mycorrhizal fungi, especially when it is difficult to gather a sufficient number of data on morphological features. Short arbitrary oligonucleotides were used as primers for the amplification of genomic DNA extracted from spores of arbuscular fungi. The RAPD fingerprints showed banding patterns which allowed us to distinguish between species and even isolates within Glomales. In order to identify mycorrhizal fungi during their symbiotic phase, a nonpolymorphic RAPD band identified as marker for some isolates ofGlomus mosseaewas purified from agarose gels and cloned in a bluescript vector. The fragment was sequenced and specific primers (PO‐M3) were designed for the mycorrhizal fungus. They specifically and successfully amplified the DNA not only fromG. mosseaespores, but also from roots of pea, clover, leek and onion plants when they were colonized byG. mosseaeisolate