An emerging field of research in soil ecology concerns the effects of aboveground biota and processes on the soil microbial community. Recent studies have documented profound effects of litter fall, litter leachates, canopy leachates, and litter chemistry on soil microbes and microbially mediated ecosystem processes. Few studies however have investigated effects of litter and litter leachates on abundance and colonization of the mutualistic arbuscular mycorrhizal fungi (AMF). We observed a negative correlation between increases in cottonwood (Populus trichocarpa) litter and AMF abundance and inoculum potential along a riparian chronosequence in northwest Montana. We investigated effects of cottonwood litter and litter extract additions on the colonization of AMF colonizing both cottonwood and Sorghum (Sorghum sudanese) seedlings. Addition of 5% dried cottonwood leaves completely inhibited AMF colonization of sorghum. Moreover, additions of aqueous litter extract significantly reduced AMF colonization of cottonwood seedlings, and reduced soil hyphal lengths. AMF colonization of sorghum was significantly negatively correlated with increasing litter extract concentrations. The effect of the litter extract on AMF colonization of sorghum did not appear to be mediated by changes in soil pH or root biomass, as there were no significant differences in these responses across the treatments. Available phosphorus was higher in soil receiving highest concentration of litter extract, but still strongly limiting to plant growth (<1ppm). This suggests secondary compounds present in cottonwood litter (e.g. polyphenolics) may affect AMF colonization. A range of polyphenolic compounds found in cottonwood litter were found to reduced AMF colonization but not affect non-mycorrhizal root colonizing fungi.. These data suggest a novel feedback between host and symbionts that would alter AMF successional dynamics, and indicate another role of polyphenolics in ecosystem processes.