Macroalgae are a potentially novel source of nutrition and biologically active molecules. Proliferative species such as Eucheuma denticulatum, Solieria chordalis (red algae) and Sargassum muticum (brown alga) constitute a huge biomass that can be exploited. In this study, we focus on the extraction of polysaccharides from these three macroalgae species and the characterization of cell wall polysaccharides such as carrageenans, fucoidans and alginates by Fourier Transform Infrared spectroscopy with Attenuated Reflectance Module (FTIR-ATR). The comparison of purified extracts with commercial solutions of fucoidans, alginates or carrageenans shows a strong similarity between the spectra. It demonstrates that the methods of extraction that have been used are also suitable purifying technics. Moreover, it validates infrared spectroscopy as a quick, simple and non-destructive method for the accurate analysis of polysaccharides. The FTIR technique applied to samples collected at different periods of the year allowed us to highlight differences in the composition of fucoidans, alginates and carrageenans. Different classes corresponding to the season can be distinguished by statistical multidimensionnal analysis (Principal Component Analysis) showing that the structure of algal polysaccharides, related to bioactivity, depends on the period of harvest. FTIR results showed that S. chordalis and E. denticulatum possess a dominant type of carrageenan called iota-carrageenan. This type of carrageenan is in the majority when the alga is at maturity in its development cycle. During its growth phase, iota-carrageenan precursors can be detected by FTIR spectra, enabling a better control of the extraction and an application of these compounds in various economic sectors. When the alga E. denticulatum is in its juvenile stage, we found traces of kappa-carrageenan and nu-carrageenan polysaccharides in some extracts.