Japanese knotweed, Fallopia japonica is an invasive alien weed causing serious environmental and economical problems in Europe and North America. During field surveys in Japan, a rust fungus was observed in summer/autumn causing severe damage to the weed. This rust pathogen was identified as Puccinia polygoni-amphibii var. tovariae based on morphology. The rust was found from August to December in a field site at Kyushu University, Fukuoka Pref., Japan. Urediniospores were observed between August and October and were associated with severe damage and defoliation of Japanese knotweed followed by teliospores were occurred in the field from November to December. The symptoms appeared 5 days after inoculation (dai) and inoculated leaves were defoliated 15 dai. It has not been confirmed if P. polygoni-amphibii var. tovariae is autoecious or heteroecious. However, it may still have potential as a biological control agent for F. japonica, and further research is needed to elucidate its life cycle and host range.