Glyphosate-tolerant cropping systems (GTS) have been used for over 10 years, and anecdotal evidence among US farmers has linked this to yield reductions which could be related to the effects of glyphosate on soil microbial communities. There is evidence that glyphosate stimulates certain fungi and manganese-oxidizing bacteria that cause Mn deficiency in crops. Some Fusarium spp. that can be pathogenic have been shown to be stimulated by glyphosate under hydroponic conditions. The objective of this study was to determine the response and diversity of Fusarium in soils during transition to GTS. A completely randomized greenhouse experiment compared two soils of the same type and chemical/physical properties - where one had been under >10 yrs of GTS and the other had never received glyphosate.  A corn-soybean rotation (mimicking 8 field yrs) was imposed in rhizoboxes (allowed sampling of intact rhizosphere soil) where each crop received 2 applications of glyphosate and crops were harvested at 60 days. Rhizosphere and bulk soil samples were taken non-destructively at 1 and 7 days after glyphosate application. Species diversity was analyzed by DGGE using primers specific to Fusarium, and the same primers were used to quantify Fusarium by qPCR. The results of this study will provide a better understanding of how glyphosate-tolerant crop systems cause changes in the soil microbial community, and if such changes foster proliferation of non-beneficial and potentially pathogenic fungi.