We performed microspectroscopic evaluation of the pigment composition of the photosynthetic compartments of both algae and higher plants. The feasibility of microspectroscopy for discriminating among species and/or phylogenetic groups was tested on laboratory cultures. Gaussian bands decompositions, and a fitting algorithm, together with fourth-derivative transformation of absorbance spectra, provided a reliable discrimination among chlorophylls, phycobiliproteins and carotenoids. Comparative analysis of absorption spectra highlighted the evolutionary grouping of the algae into three main lineages in accordance with the most recent endosymbiotic theories.