The chloroplast ATP synthase/ATPase (cpATPase) couples ATP synthesis to the light-driven electrochemical proton gradient. The cpATPase is a multi-protein complex and consists of a membrane-spanning protein channel (comprising subunit types a, b, b' and c) and a peripheral domain (subunits α, β, γ, δ and ε). We report the characterization of the Arabidopsis thaliana CGL160 (AtCGL160) protein, conserved in green algae and plants. AtCGL160 is an integral thylakoid protein and its C-terminal portion is distantly related to prokaryotic Atp1/UncI proteins which are thought to function in ATP synthase assembly. Plants without AtCGL160 display an increase in xanthophyll-cycle activity and energy-dependent non-photochemical quenching (qE). These photosynthetic perturbations can be attributed to a severe reduction in cpATPase levels which result in increased acidification of the thylakoid lumen. AtCGL160 is not an integral cpATPase component, but is specifically required for the efficient incorporation of the c-subunit into the cpATPase. AtCGL160, as well as a chimeric protein containing the N-terminal part of AtCGL160 and Synechocystis sp. PCC6803 Atp1, physically interact with the c-subunit. We conclude that AtCGL160 and Atp1 facilitate assembly of the membranous part of the cpATPase in their hosts, but loss of their functions provokes a unique compensatory response in each organism.