We compared the photosynthetic and photoassimilate transport responses of Melaleuca cajuputi Powell seedlings to root hypoxia with those of Eucalyptus camaldulensis Dehnh. Control and hypoxia treated roots were maintained in a nutrient solution through which air or nitrogen was bubbled. Under root hypoxic conditions, seedlings of M. cajuputi, a flood-tolerant species, maintained height growth, whereas seedlings of E. camaldulensis, a moderately flood-tolerant species, showed markedly decreased height growth compared with control seedlings. Root hypoxia caused decreases in whole-plant biomass, photosynthetic rate and stomatal conductance in E. camaldulensis, but not in M. cajuputi. Photoassimilate transport to roots decreased significantly in E. camaldulensis seedlings 4 days after treatment and starch accumulated in mature leaves. Photoassimilate supply to hypoxic roots of E. camaldulensis seedlings was, thus, limited by reduced photoassimilate transport rather than by reduced photosynthesis. In contrast, M. cajuputi seedlings showed sustained photoassimilate transport to hypoxic roots and persistent photosynthesis, which together provided a substantial photoassimilate supply to the roots. Sucrose accumulated in hypoxic E. camaldulensis roots, but not in hypoxic M. cajuputi roots. A stable, low sucrose concentration in hypoxic roots would let M. cajuputi seedlings prolong photoassimilate transport to the roots. Photoassimilate partitioning among the water-soluble carbohydrates, starch and structural carbohydrates within the roots was unaffected by root hypoxia in E. camaldulensis, but in M. cajuputi, partitioning was shifted somewhat from structural carbohydrates to water-soluble carbohydrates. This suggests that M. cajuputi seedlings are able to increase photoassimilate utilization in metabolism and sustain energy production under root hypoxic conditions.