To understand how yellow lupin tolerates waterlogging better than narrow-leafed lupin, we investigated the roles of the roots and the shoots of these species. Reciprocal- and self-grafted combinations (scion = shoot/rootstock) of yellow and narrow-leafed lupin were made at the 2-leaf stage and waterlogged 45 days later (8-10 leaf stage). Responses to waterlogging were examined at the end of waterlogging and following a recovery period of 14 days.Waterlogging of reciprocal and self-grafted plants reduced total plant dry weight by 15-58% compared with non-waterlogged controls. These reductions were greater when the rootstock was narrow-leafed rather than yellow lupin, and were similar for the roots and shoots. Waterlogging increased dry weight of hypocotyl roots in most grafting combinations (by 2-19-fold), but grafts with narrow-leafed lupin scions produced almost twice the hypocotyl root length of grafts with yellow lupin scions. During the waterlogging period, leaf gas exchange decreased by 16-74% in all grafting combinations except in narrow-leafed lupin scion/yellow lupin rootstock where it increased by 17-30%. During waterlogging, stem water potential decreased and leaf osmotic pressure increased. These changes compensated one another and consequently there was no effect on bulk leaf turgor. After 14 days recovery, water relations returned to initial values.Tolerance of the whole plant to waterlogging was influenced more by the root genotype than the shoot genotype. However, production of hypocotyl roots in response to waterlogging was related to the shoot genotype rather than the root genotype.