Rice plants cope with flash floods using either an ‘escape strategy’ involving rapid shoot elongation or a ‘quiescence strategy’ involving survival underwater with minimal activity. To clarify the differences in the response of leaf photosynthesis properties to conditions during and after submergence, two rice cultivars were compared: a non-shoot-elongating cultivar IR 67520-B-14-1-3-2-2 (IR67520) and a shoot-elongating cultivar IR72442-6B-3-2-1-1 (IR72442). Twenty-three-day-old seedlings were submerged in 80-cm-deep water for 14 days. During submergence, the chlorophyll contents of the upper fully expanded leaf (5th leaf) and newly developed leaf later (6th leaf) and the maximal quantum yield of photosystem II (Fv/Fm) of the fifth leaf decreased earlier in IR72442 than in IR67520. In the submerged sixth leaf, Fv/Fm was higher in IR72442 than in IR67520 at early measurement. Although Fv/Fm of the sixth leaf in submerged IR67520 increased substantially from 2 days post-submergence, IR72442 decreased because of leaf chlorosis. Therefore, a non-shoot-elongating cultivar coped with submergence by inhibiting photodamage and maintaining high chlorophyll content in the leaves. The shoot-elongating cultivar was able to maintain the photosynthetic capacity of the newly developed leaf during submergence by prompt reduction of chlorophyll and chlorophyll fluorescence in the leaf that developed before submergence.