Abstract: Specific primers and Polymerase Chain Reaction (PCR) assays that identify Arbuscular Mycorrhizal (AM) fungi Glomus intraradices were developed. Monoxenic cultures of fungi G. intraradices and Gigaspora gigantea in association with Ri T-DNA transformed carrot roots were established in order to obtain fungal DNA free of host and others contaminants. RAPD analysis using 10 AM fungi from genera Glomus, Gigaspora and Acaulospora allowed the determination of two amplified fragments that were specific to G. intraradices. The DNA fragments were cloned, sequenced and subsequently used to design SCAR species-specific primers. A set of primers, GIN630F and GIN630R, drove the amplification of a 630 bp fragment specific for G. intraradices, which was absent when DNA of other AM fungi or plants were used as templates. The assay allowed the detection of G. intraradices in colonized roots of carrot. The SCAR-based protocol described here may be a tool of great value in studies of Glomeromycota`s molecular systematic and ecology.