In situ gene amplification (in situ PCR) is a recent, powerful molecular technique which allows the localization of low abundance nucleic acids targets directly within tissue sections. The work presented here is, to our knowledge, the first report of successful direct detection of in situ PCR amplification with fluorescently-labelled primers, and the first successful in situ PCR performed on arbuscular mycorrhizal (AM) fungi. Ribosomal SSU genes within AM fungal spore sections were amplified by using fluorescent, glomalean-specific primers, then directly detected by means of epifluorescence microscopy. Different controls confirmed the successfulness of the in situ amplification. These results open new avenues in the study of arbuscular mycorrhizas, where genetic processes seem to be transient and very localized.