Glyphosate-tolerant cropping systems (GTS) have been in widespread use 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, some of which are known to be pathogenic. These have been shown to be stimulated by glyphosate under hydroponic conditions, but not yet under field conditions. The objective of this study was to determine the response and diversity of microorganisms in soils during transition to GTS. A completely randomized greenhouse experiment was designed to compare 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 where each crop received 2 applications of glyphosate and crops were harvested at 60 days. After harvesting, residue samples were placed in fresh aliquots of the same soils used in the greenhouse. Residues were allowed to incubate for 30 days, with destructive sampling at 3, 7, and 30 days. PLFAs were extracted from the samples and analyzed via gas chromatography in order to assess the changes in PLFA diversity stemming from the decomposition of GT and non-GT soybean residue in both soils. The results of this study will provide a better understanding of how glyphosate-tolerant crop systems cause changes in the soil microbial community.