The arbuscular mycorrhizal (AM) fungus Glomus intraradices was grown in vitro with RIT-DNA transformed Daucus carota roots on plates divided into two compartments. One side of the plates contained only fungal hyphae and spores while the other contained mycorrhizal roots. Using this technique, the limitations of insufficient biological material available for molecular analysis of this obligate symbiont were overcome. Fungal material from the first compartment was used as a pure source of G. intraradices for genomic DNA extraction. PCR amplification as well as southern hybridization were conducted using this DNA. Sufficient pure genomic DNA and mRNA was obtained to carry out Southern analysis, achieve optimum PCR results with 25–35 cycles and conduct RT-PCR. Differential expression of chitin synthase class I and II was detected in G. intraradices. Using degenerate primers specific to fungal chitin synthase sequences, a single amplification product obtained after 25 cycles of PCR was cloned. Sequencing of this fragment revealed similarity to other fungal chitin synthase genes. PCR with these primers and additional primers allowed the amplification of chitin synthase fragments from spores of different isolates of G. intraradices as well as from G. mosseae, Gigaspora margarita, Acaulaspora scrobiculata, Scutellospora calospora and Entrophosphora colombiana. A total of 21 chitin synthase sequences from different species and isolates of various AM fungi were successfully amplified. Sequencing of these fragments permitted their classification into class I and II of the chitin synthase groups.