The excitation spectra of chlorophyll (Chl) fluorescence can be used to differentiate phytoplankton populations at phylum level in vivo and in situ within a few minutes. The investigated phytoplankton divisions (Dinophyta, Bacillariophyta, Chrysophyta, Cyanophyta, Cryptophyta, Chlorophyta) are each characterized by a specific composition of photosynthetic antenna pigments and, consequently, by a specific excitation spectrum of the Chl fluorescence. Norm excitation spectra (emission of 680 nm and excitation of 400-600 nm) of every division were obtained from several species per division by a F4500 fluorescence spectrophotometer. Fisher's linear discriminant analysis of the norm spectra shows that the divisions could be discriminated. The discrimination method, established by multivariate linear regression and weighted least squares, was used to differentiate the phytoplankton samples cultured in the laboratory and samples collected from the Jiaozhao Bay at division level. The correctly discriminated samples were more than 94% for single algal species ones, more than 84% for simulatively mixed ones, more than 83% for real mixed ones and 100% for samples collected from the Jiaozhou Bay for the dominant species. The method for phytoplankton differentiation described here can be applied to routine checking by fluorescence spectrophotometer, and benefit the monitoring and supervision tasks related to phytoplankton populations in the marine environments.