Optical properties of eight algae species were measured on a flow cytometer. Forward and perpendicular light scatter measurements provide information on the size and shape of algae cells. The intensity of chlorophyll fluorescence varies greatly among the studied algae species and can be used to distinguish them. Measurements of chlorophyll fluorescence after excitation with different wavelengths provide a fluorescence excitation spectrum for each species over the available wavelength range. These spectra reflect the different photosynthetic pigment contents of the species. Staining algae cells with the DNA stains, Hoechst 33342 and DAPI, provides two additional optical parameters to distinguish algae populations: blue nuclear fluorescence and yellow granular fluorescence. The combination of these optical measurements enables the distinction of each algae species into a small cluster in a hyperspace of parameters. The automation of phytoplankton analysis on the flow cytometer may lead to the rapid and objective assessment of water quality.