The analysis and identification of a wide range of secondary metabolites biosynthesized by different algal taxa and cyanobacteria has been performed through a selective and sensitive methodology, mainly based on reversed-phase HPLC coupled both to UV photodiode array detection and to atmospheric pressure mass spectrometric techniques (HPLC-DAD-APIMS). Results are reported here with special attention to the analyses carried out both on the natural phytoplankton (mixed populations) of Lake Tovel (Northern Italy, Brenta Dolomites) and on enclosure-produced biomass of the dinoflagellate Glenodinium sanguineum Marchesoni (1941). This analytical procedure might represent a powerful tool for the fast screening of the taxonomic composition (broad groups, e.g. divisions) of natural mixed populations of phytoplankton, by providing a reliable distribution of accessory pigments extracted from microalgae, such as carotenoids and chlorophyll derivatives. Furthermore, we showed that in the same chromatographic analysis other classes of natural products, such as galactolipids, alkaloids, sterols and mycosporine-like amino acids, can be detected by using combined optical and mass spectrometric techniques. These metabolites represent distinctive biochemical signatures, sometimes even at the species level.