The rust pathogen, Puccinia thlaspeos, is used for biocontrol of dyer's woad. Rust infection results in chlorotic leaves and abnormal flower and seed production of this noxious weed during its second year of growth. Auxin-like and cytokinin-like activity of healthy and infected plants (roots, shoots, and leaves) were determined during different growth stages. These samples were analyzed by use of the mung-bean rooting bioassay (auxin-like activity) and the soybean-callus bioassay (cytokinin-like activity). Rooting activity in the mung-bean bioassay was significantly higher in the infected-root extracts from Harvest 1 (rosette stage) compared with the healthy-root extracts and significantly higher in the healthy-shoot extracts from Harvest 2 (bolting plants) compared with infected-shoot extracts. Infected plants collected during Harvest 1 had greatly reduced cytokinin-like activity in the roots, shoots, and leaves compared with the healthy plants. Cytokinin-like activity increased slightly in the infected plants collected in subsequent harvests, with the highest activity recorded in root extracts. The results suggest potential ways that the rust-causing fungal pathogen is able to influence some physiologic processes in dyer's woad and so affect its growth.