Gradients of photoinhibition within a leaf caused by different color lights were studied to get more insight into the controversy whether photon absorption by chlorophyll or Mn is the primary cause of photoinhibition, suggested by the excess-energy hypothesis or the Mn (two-step) hypothesis, respectively. We photoinhibited lincomycin-treated leaf-discs with white, blue, green or red light. A combination of a micro-fiber fluorometer, a fiber-thinning technique and a micro-manipulator enabled us to measure the chlorophyll fluorescence signals within a leaf. Gradients of photoinhibition were also compared with results from various conventional fluorometers to estimate their depth of signal detection. The photoinhibition was more severe in the descending order of blue, red and green light near the adaxial surface, and in the descending order of blue, green and red light in the deeper tissue, which is correlated with the absorption spectrum of chlorophyll and Mn, respectively. These results cannot be explained by either hypothesis alone and strongly suggest that both mechanisms occur in photoinhibition. Fv/Fm values of photoinhibited leaves estimated with the conventional fluorometers were different from the whole tissue. This is because the depths, in which these systems detect fluorescence signals, differ depending on the wavelengths of measuring beam and detector.