This Special Issue is based on the 7th Conference of the International Society for Plant Anaerobiosis (ISPA), held in Nijmegen, The Netherlands, 12–16 June 2001. The papers describe and analyse many of the responses that plants display when subjected to waterlogging of the soil or deeper submergence. These responses may be injurious or adaptive, and are discussed at various levels of organizational complexity ranging from ecosystem processes, through individual plants to single cells. The research incorporates molecular biology and genetics, cell physiology, biochemistry, hormone physiology, whole plant physiology, plant demography and ecology. The study of the damage to young rice plants caused by submergence, especially as experienced in the rainfed lowlands of Asia, is comprehensively addressed. This work integrates various specialized approaches ranging from agronomy to molecular genetics, and demonstrates how plant biology can be harnessed to improve stress tolerance in an important crop species while simultaneously improving basic understanding of tolerance mechanisms and plant processes.