Two-dimensional Fourier-transform-based pattern recognition is used to characterize natural populations of marine algae by their two-dimensional,in vivofluorescence spectra. The two dimensional fluorescence spectrum, termed an excitation-emission matrix (EEM), is acquired using a portable, multichannel fluorescence spectrophotometer (PMFS). Natural populations in the Gulf of Mexico south of Louisiana and the coastal area near Savannah, Georgia are characterized by their measurement ofin situfluorescence. Characterization of unknown populations is achieved by comparing the unknown EEMs to a collection of standard EEMs acquired from 23 species (6 classes) of marine algae. Pattern recognition results from data collected along the Georgia coast indicating diatom populations were confirmed by microscopic examination of selected samples.