Chlorophyll fluorescence imaging is a non-invasive method to monitor the metabolic state of photosynthetic organisms. We used spatially resolved (imaging) microscopic measurements of chlorophyll fluorescence kinetics to follow the fate of individual cells of the filamentous brown alga Pylaiella littoralis infected by the biotrophic parasite Chytridium polysiphoniae (Chytridiomycota). These measurements showed strong differences between individual parameters of the inhibition of photosynthesis, revealing important details about the mechanism of damage. The dark-adapted photochemistry of photosystem II itself (measured as F v /F m , where F v ¼ F m À F 0 ) remained unaffected until a very late stage of damage to the cell, while the light-adapted efficiency of PSII electron transport decreased earlier. A particularly complex pattern was found for the changes in nonphotochemical quenching (NPQ). The shape of the fluorescence transients suggests that the changes in NPQ during the actinic light period are caused by changes in F 0 . The infection affected NPQ directly after the onset of the actinic light period more than in the steady state of photosynthesis. These results indicate that the infection affects the regulation of energy dissipation (e.g. by changes in antenna coupling). In early infection stages, NPQ increased, which is reflected by an increase in the 'vitality parameter' (relative fluorescence decrease, defined as (F p À F s )/F s ). In the second half of the infection process, all photosynthetic parameters declined, including the efficiency of photosystem II as measured by F v /F m , and NPQ.