We investigated the effects of epiphytes on photosynthetic activity in a seagrass, Zostera marina. Parameters in our chlorophyll (Chl) fluorescence imaging technique, including Fo, Fm, and Fv/Fm, were monitored from leaf surfaces before and after those epiphytes were removed. Because of the uneven distribution of light intensities, Fm values at the margin of an image were underestimated while those in the central region were overestimated. Chl fluorescence emissions from all leaves except the youngest one were altered by the presence of epiphytes, which predominantly inhabited the surfaces of older leaves. Only a few were found lower on the plant where leaves were very close to each other. Regions where the epiphytes had been loosely bound before their gentle removal showed full restoration of photosynthetic performance to control levels afterward. However, only minor recovery of photosynthesis was found in areas that had been riddled with tightly bound epiphytes and were permanently damaged. In years 2002 and 2003, leaf productivity peaked in May and plummeted in November. More epiphytic diatoms were distributed when the seagrass biomass was larger, with pinnate diatoms dominating.