Fusarium equiseti and F. pallidoroseum are frequently reported as secondary colonizers of plant tissues. In this study they were isolated from the embryos of weathered cottonseed. Most isolates tested produced equisetin, an antibiotic, when grown on potato dextrose agar, rice, surface-sterilized cottonseed, or autoclaved cottonseed. This is the first report of equisetin from F. pallidoroseum. Equisetin was extracted from cultures of F. equiseti and F. pallidoroseum with acetone and dichloromethane, and partially purified by TLC. Two epimers of equisetin, designated as EQ and epi-EQ, were separated by HPLC. EQ or epi-EQ at 2·5–10 μg ml−1 suppressed germination or inhibited growth of various monocotyledonous and dicotyledonous seed, when the seed were incubated at 30°C under aqueous shake conditions. The two epimers also inhibited the growth of young seedlings and caused necrotic lesions on the roots, cotyledons, and coleoptiles of tested plant seedlings. The results suggest that equisetin may be a pathogenic factor of F. equiseti and F. pallidoroseum on seed and seedling health of cotton and other plants.