Seeds of green foxtail [Setaria viridis (L.) P. Beauv. # SETVI] and giant foxtail (S. faberi Herrm. # SETFA) were collected from mature plants in the field and recovered from three soil depths under two types of tillage. Fungi colonizing the caryopses were isolated to determine the effect of tillage and soil depth on fungal colonization and the field flora. Alternaria alternata (Fr.) Keissler and Epicoccum purpurascens Ehrenb. ex Schlecht. were the two fungi most frequently isolated from the hand-harvested seeds. Percentages of fungal colonization were directly related to size of the caryopses. The most frequently isolated fungus species recovered from seeds from soil were A. alternata, Cladosporium cladosporioides (Fresen.) de Vries, E. purpurascens, and two unidentified fungi with sterile mycelium. One sterile fungus had white rough mycelium, and the other had dark mycelium. These two sterile fungi had a detrimental effect on foxtail seed germination in the laboratory. Caryopsis colonization seems to be related to the placement of the crop residues in the soil. In reduced-tillage plots, more caryopses were colonized in the top soil layer (0 to 7.5 cm) than in the 7.5- to 15-cm layer. In plowed soils, greater colonization occurred at the lower depth.