Alternaria crassa, a mycoherbicide for jimsonweed control, was tested for differential effects on growth, infectivity, and phenolic metabolism of two field-collected jimsonweed varieties. Seeds from field-grown red- and green-stemmed jimsonweed varieties were grown in the greenhouse and spores were applied in aqueous solutions. Infection studies showed no significant differences between the two weed varieties when tested at various growth stages from cotyledonary to 8–leaf stage at 2.5 × 104 spores ml−1. Spore dose response tests with A. crassa spores (6.25 to 100 x 103 spores ml−1) showed no significant varietal differences in disease ratings. Extractable phenylalanine ammonia-lyase activity increased nearly equally (2- to 3-fold above control) in both varieties (8- to 9-leaf stage) 48 to 72 h after treatment with 5 × 104 spores ml−1. The only significant differences between treated varieties occurred 72 h after treatment. Exposure to A. crassa lowered total ethanol-soluble phenolic levels in both varieties 72 h after treatment. Spectrophotometric scans (400 to 700 nm) of ethanol extracts (72 h after treatment) indicated that infection caused some absorbance increases, especially in red-stemmed jimsonweed. Anthocyanin content was about 11-fold higher in red-stemmed than green-stemmed jimsonweed, and A. crassa treatment slightly increased the anthocyanin absorption peak of the red-stemmed variety.