Abstract: Identification of algae in water samples is carried out with a flow cytometer having at least one high intensity light source to provide a light path such as a laser, means for passing the algae through the light path and a system of detectors arranged to measure chlorophyll fluorescence and at least two other parameters such as forward light scattering, perpendicular light scattering, backward light scattering, pulse length and/or shape of the scattered signals, fluorescence and pulse length and/or shape of the fluorscence signals. In order to separate the light output from the flow cytometer into components which can yield useful measurements, a system of partially reflecting mirrors and dichroic mirrors is used. Preferably, the high intensity light source is two independent lasers having parallel light paths one of which is separated in a UV range and the other in an all lines mode.