Rice (Oryza sativa L.) is the only cereal that can be cultivated in the frequently flooded river deltas of South-East and South Asia. The survival strategies used by rice have been studied quite extensively and the role of several phytohormones in the elongation response has been established. Deep-water rice cultivars can diminish flooding stress by rapid elongation of their submerged tissues to keep up with the rising waters. Other rice cultivars may react by mechanisms of submergence tolerance. Aerenchyma and aerenchymatous adventitious roots are formed that facilitate oxygen diffusion to prevent anaerobic conditions in the submerged tissues. This paper discusses the molecular aspects of the mechanism that leads to shoot elongation (leaves of seedlings and internodes), the regulation of which involves metabolism of, and interactions between, ethylene, gibberellins and abscisic acid. Finally, the importance of new techniques in future research is assessed. Current molecular technology can reveal subtle differences in gene activity between tolerant and non-tolerant cultivars, and identify genes that are involved in the regulation of submergence avoidance and tolerance.