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Two-dimensional Fourier transform based pattern recognition is used to characterize natural populations of marine algae by their two-dimensional, in vivo fluorescence spectra. The two-dimensional fluorescence spectrum is called and excitation-emission matrix (EEM) and is acquired by 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 in-situ fluorescence. 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 the data collected along the Georgia coast was confirmed by microscopic examination of selected samples. Keywords: fluorescence analysis; marine analysis; marine algae; Fourier spectroscopy.