The effects of Bt crops on non-target biota in agroecosystems have been studied extensively. Most research has concluded that Bt crops have very little impact on non-target arthropods. By considering the magnitude of these effects relative to the impacts of other agricultural manipulations we can begin to prioritize our research focus for arthropod biodiversity studies in these systems. This project examines the effects of Bt cotton on non-target arthropod communities relative to the effects of tillage and cover crop identity. Over a two year period, arthropod samples were collected from four cropping cycles on a 2 acre cotton farm in Athens, GA. Sampling methods included sweep netting, pitfall trapping, and heat extraction from soil cores. All arthropods were identified to the family level and were then analyzed at the whole community, and individual family levels using non-metric multidimensional scaling and indicator species analysis (PC-ORD). Upon examining the relative magnitude of all effects tillage appeared to be the dominant factor affecting whole communities followed by cover crop identity and finally cotton type. The same was found for analyses of individual taxa however, there was a high degree of variability among sampling dates in terms of which taxa were significantly affected. These results not only confirm that Bt crops play an insignificant role in shaping arthropod communities but further suggest that we put more emphasis in studies examining the impact of tillage. This study also stresses the importance of conducting analyses beyond the whole-community level when studying arthropod biodiversity in agroecosystems.