The impact of alder Phytophthora (Phytophthora alni subsp. alni) on corticular photosynthetic metabolism was explored via measurements of chlorophyll fluorescence. Stem inoculation induced a sharp reduction of maximum (Fv/Fm) and effective quantum yield of PSII (Symbol). Observations of the axial and radial spread of the pathogen revealed that near to the point of inoculation and in the whole centre of the stem lesion Fv/Fm and Symbol of the cortex chlorenchyma decreased to almost zero, indicating tissue necrosis. Low values of Fv/Fm and Symbol were also found in some presymptomatic regions beyond the visible stem lesion. In contrast, substantial photosynthetic activity was found in uninvaded parts of the inoculated trees and in the control. These stem parts showed a marked light-adapted quantum efficiency of PSII as well as marked electron transport rates in their bark tissues. Thus, corticular photosynthesis stayed unaffected in these stem parts supporting stem carbon balance. Chlorophyll fluorescence measurements in the field illustrated that stem infection with P. alni subsp. alni and the effect on the bark tissues is not only highly heterogeneous but also underlies very quick temporal changes, due to a rapid destruction of the photosynthetic apparatus. The results show that chlorophyll fluorescence measurements and fluorescence imaging are useful indicators of tissue infection caused by Phytophthora infection of bark tissues. Chlorophyll fluorescence measurements can be used to map and visualize the spatial as well as temporal spread of bark pathogens and can give a first indication of invasion of the host tissue beyond the visible lesion.