In recent years, much interest has been focused on the biotechnological potential of microalgae, mainly due to their rapid growth and the identification of several substances synthesized by these organisms. The isolation and in vitro cultivation of native microalgae species is very important for taxonomic and conservation studies and is the first step towards feasibility studies of local commercial productions. In this study 114 isolates of microalgae were obtained from samples collected in 23 locations of the island of São Miguel, Azores. From them, 60 species were identified comprising 39 Chlorophyta, 10 Ochrophyta, 6 Cyanophyta, 3 Charophyta, 1 Euglenozoa and 1 Cryptophyta. Eighteen of the species identified constitute new records for the Island of São Miguel.