In a previous study (Carrera et al., submitted for publication) we found that soil microbial community structure was distinctly different under plasticulture than under hairy vetch cover crops in tomato production systems. In order to determine the major factors affecting microbial communities we set up a replicated field experiment with nine treatments: bare soil, black polyethylene, white polyethylene, hairy vetch cover crop, hairy vetch above-ground biomass, hairy vetch below-ground biomass, rye cover crop, rye above-ground biomass, and rye below-ground biomass. Soil temperature and moisture were monitored. Tomato rhizosphere and bulk soil were sampled and PLFA analyzed. The black polyethylene treatment had the highest soil temperatures, while both black and white polyethylene treatments had the highest soil moisture levels. Soil and rhizosphere microbial community structure were significantly different for black and white polyethylene compared to all other treatments, suggesting that soil temperature is not a major factor while soil moisture might be. Vetch shoots had more impact on microbial communities than vetch roots, while rye roots had more impact than rye shoots.