While the importance of cortical aerenchyma in flood tolerance is well established, this pathway for gaseous exchange is often destroyed during secondary growth. For woody species, therefore, an additional pathway must develop for oxygen to reach submerged tissues. In this paper we examine the potential for the aerenchymatous phellem (cork) of Lythrum salicaria L. to provide a pathway for gas transport from shoots to roots and assess its importance in flood tolerance. Plants in which the continuity of the aerenchymatous phellem between shoots and roots was broken showed a significant reduction in oxygen levels in roots, but no difference in carbon dioxide levels compared with controls that retained an intact phellem. These plants also had a greater total shoot height and shoot dry weight, and an increase in shoot/root dry mass ratios compared with controls. Total dry weight was not significantly affected by this treatment. This study is the first to show that the aerenchymatous phellem can provide a pathway for gaseous exchange between roots and shoots and can influence plant morphology and patterns of resource allocation. This suggests that this tissue may play a significant role in the flood tolerance of a woody plant.