We have screened the genome of ecto- and endo-mycorrhizal fungi by using primers designed on microsatellite sequences: (CT)8, (CA)8, (GACA)4, (TGTC)4, (GTG)5. PCR experiments proved that microsatellites such as (GTG)5 exist as short repeated sequences in 11 species of Tuber (Ascomycetes) and seven species within Glomales (Zygomycetes). Variations in the banding pattern obtained by DNA fingerprinting enabled all these species and some isolates to be distinguished according to the number, size and intensity of the fragments. (GACA)4 and (TGTC)4 also led to successful amplifications in some isolates from Tuber and Glomales. These experiments demonstrate that microsatellite primers are reliable, sensitive and technically simple tools for assaying genetic variability in mycorrhizal fungi, and can be used to discriminate mycorrhizal symbionts with different taxonomic features. (GTG)5 in fact led to species-specific fingerprints in both truffles, which are closely related species, and in Glomales, which are quite separate species in evolutionary terms.