The selectivity of fluorescence spectroscopy is exploited for the characterization of marine algae. Two-dimensional, digital images of in vivo fluorescence intensity versus excitation and emission wavelengths, called excitation-emission matrices (EEMs), are used as spectral "fingerprints" for marine phytoplankton populations. Fourier-transform-based pattern recognition is described along with its inherent strengths and weaknesses for the analysis of natural populations. The EEMs of unknown algae are compared to a library of standard EEMs representing 23 algal species and 6 classes with better than 80% accuracy. The EEMs acquired under different physiological conditions are used in determining pattern recognition reliability. The potential for fingerprinting mixed populations and oceanographic regions is also discussed.