This dataset was created as a part of an experiment which used a soybean-corn intercrop system for examining how the community structure of agricultural weeds changes with fertilization and with the identity of the crop species. The composition of the weed flora in intercrops was compared with the weed flora of the respective sole crops, with and without fertilization. The experiment was conducted at Kellogg Biological Station (KBS) in southwestern Michigan, USA, in 1993.