Integrating perennial grasses into row crop rotations have proved to be sustainable owing to enhanced soil physical and chemical properties that are primarily attributed to greater organic matter, greater diversity of plant residues, efficient nutrient cycling, lower soil compaction, greater proportion of soil macroaggregates and fungal populations. Microbial communities play a central role in all of these processes and are greatly influenced by management practices. We used the automated ribosomal intergenic spacer analysis (ARISA) to study bacterial and fungal community shifts as affected by the type of crop rotation. We compared a four year crop rotation (comprising two years of perennial bahiagrass (Paspalum notatum Fluegge) followed by a year each of peanut and cotton) with a three year crop rotation (comprising a year of peanut followed by two years of cotton). We also compared the 4 year crop rotation with and without cattle grazing to see the effects of grazing on microbial communities. Statistical analyses including MANOVA and CCA using relevant biogeochemical parameters revealed that unlike parameters like biomass C, nutrient cycling enzymes, organic C, microbial communities were influenced by the crop more than the rotation itself. However, the two consecutive years of bahiagrass seemed to promote greater fungal populations as compared to other crops. Likewise, grazing itself did not significantly affect microbial communities as compared to other biogeochemical factors.