Excitation-emission fluorescence matrices of phytoplankton communities were simulated from laboratory-grown algae and cyanobacteria cultures, to define the optical configurations of theoretical fluorometers that either minimize or maximize the representation of these phytoplankton groups in community variable fluorescence measurements. Excitation sources that match the photosystem II (PSII) action spectrum of cyanobacteria do not necessarily lead to equal representation of cyanobacteria in community fluorescence. In communities with an equal share of algae and cyanobacteria, inducible PSII fluorescence in algae can be retrieved from community fluorescence under blue excitation (450-470 nm) with high accuracy (R (2) = 1.00). The highest correlation between community and cyanobacterial variable fluorescence is obtained under orange-red excitation in the 590-650 nm range (R (2) = 0.54). Gaussian band decomposition reveals that in the presence of cyanobacteria, the emission detection slit must be narrow (up to 10 nm) and centred on PSII chlorophyll-a emission (similar to 683 nm) to avoid severe dampening of the signal by weakly variable phycobilisomal fluorescence and non-variable photosystem I fluorescence. When these optimizations of the optical configuration of the fluorometer are followed, both cyanobacterial and algal cultures in nutrient replete exponential growth exhibit values of the maximum quantum yield of charge separation in PSII in the range of 0.65-0.7.