In fluorometric phytoplankton analysis, the detection of red cyanobacteria is hampered by acclimation processes of the cyanobacterial photosynthetic apparatus and spectral interferences with Cryptophyta. In order to overcome these problems, a simplified energy distribution model accounting for energy pathways in the red cyanobacterial photosynthetic apparatus and the apparatus of Cryptophyta was developed. Mathematical equations were derived that enabled calculation of the pigment content of Cryptophyta and red cyanobacteria in the same sample. Phytoplankton samples were excited with 7 excitation wavelengths and measured at 4 detection wavelengths (600, 620, 650 and 685 nm) in vivo. A non-linear fit procedure accounted for variations in the fluorescence excitation spectra of red cyanobacteria and Cryptophyta in the presence of other phytoplankton fluorescence signals. Comparison with chemical pigment estimations verified that the fluorometric pigment estimation yielded reasonable results, even in the presence of energy-state transitions.