An important factor in photosynthetic ecophysiology is the light regime that a photobiont is acclimated to exploit. In a wide range of cyanobacteria and cyano-lichens, the easily measured fluorescence parameters, coefficient of nonphotochemical quenching of photosystem II variable fluorescence (q,) and nonphotochemical quenching, decline to a minimum near the acclimated growth light intensity. This characteristic pattern predicts the integrated light regime to which populations are acclimated, information that is particularly useful for cyanobacteria or cyano-lichens from habitats with highly variable light intensities. q, reflects processes that compete with photosystem II photochemistry for absorbed excitation energy. In cyanobacteria, we find no evidence for energy-dependent quenching mechanisms, which are the predominant components of q, in higher plants. Instead, in cyanobacteria, q, correlates closely with the excitation flow from the phycobilisome to photosystem I, indicating that q, reflects the state transition mechanism for equilibration of excitation from the phycobilisome to the two photosystems.Chlorophyll fluorescence analysis is a useful monitor of photosynthesis, because it is noninvasive, sensitive, and scalable over large ranges of time, light, and distance. For natural samples, fluorescence signals are specific to photobionts and allow in situ measurements of small or dilute mixed natural populations. Chlorophyll fluorescence quenching analysis has been widely applied to characterize photosynthetic metabolism in cyanobacteria and cyanolichens (Lange et al., 1989;Miller et al