Investigations were carried to unravel mechanism(s) for higher tolerance of floating over submerged leaves of long leaf pondweed (Potamogeton nodosus Poir) against photoinhibition. Chloroplasts from floating leaves showed ~5- and ~6.4-fold higher Photosystem (PS) I (reduced dichlorophenol-indophenol → methyl viologen → O2) and PS II (H2O → parabenzoquine) activities over those from submerged leaves. The saturating rate (V max) of PS II activity of chloroplasts from floating and submerged leaves reached at ~600 and ~230 µmol photons m(-2) s(-1), respectively. Photosynthetic electron transport rate in floating leaves was over 5-fold higher than in submerged leaves. Further, floating leaves, as compared to submerged leaves, showed higher F v/F m (variable to maximum chlorophyll fluorescence, a reflection of PS II efficiency), as well as a higher potential to withstand photoinhibitory damage by high light (1,200 µmol photons m(-2) s(-1)). Cells of floating leaves had not only higher mitochondria to chloroplast ratio, but also showed many mitochondria in close vicinity of chloroplasts. Electron transport (NADH → O2; succinate → O2) in isolated mitochondria of floating leaves was sensitive to both cyanide (CN(-)) and salicylhydroxamic acid (SHAM), whereas those in submerged leaves were sensitive to CN(-), but virtually insensitive to SHAM, revealing the presence of alternative oxidase in mitochondria of floating, but not of submerged, leaves. Further, the potential of floating leaves to withstand photoinhibitory damage was significantly reduced in the presence of CN(-) and SHAM, individually and in combination. Our experimental results establish that floating leaves possess better photosynthetic efficiency and capacity to withstand photoinhibition compared to submerged leaves; and mitochondria play a pivotal role in protecting photosynthetic machinery of floating leaves against photoinhibition, most likely by oxidation of NAD(P)H and reduction of O2.