A model system was developed for the molecular analysis of plant–mycorrhizal fungus interactions using Hordeum vulgare cv. Galleon and Glomus intraradices Schenk and Smith. High levels of early-colonization stage mycorrhizas (20–35% of the total root length) were routinely obtained in the roots of 12–14-d-old barley seedlings. Detailed colonization studies showed that most colonization occurred in the first 5–10 lateral roots, and that colonization in primary roots and younger lateral roots was low. Differential screening of a cDNA library prepared from the highly colonized region of the root system and subsequent northern analyses identified four differentially expressed cDNA clones. Two clones, BMR6 and BMR78, detect RNA transcripts that accumulate to much higher levels in mycorrhizal roots than in non-mycorrhizal root tissues. DNA hybridization analysis confirmed that both of the clones were of plant rather than fungal origin. Hybridization and sequence analysis strongly suggests that BMR78 represents a partial cDNA of a low copy proton-ATPase gene. This finding is consistent with the extensive proliferation of the periarbuscular membrane and high ATPase activity associated with it. BM6 detects a low copy gene whose function is unknown.