In this work, chiral and nonchiral MEKC methods have been combined with LIF detection (MEKC-LIF) to identify and quantify a group of D- and L-amino acids (D/L-aa) in different microalgae samples. The combination of the nonchiral and chiral-MEKC-LIF methods made the identification of the microalgae amino acids easier, previously derivatized with FITC, providing a double proof on the correct detection of these analytes. Three microalgae species, Spirulina platensis, Dunaliella salina, and Tetraselmis suecica, were compared in terms of their content in D-Arg, L-Arg, D-Lys, L-Lys, D-Ala, L-Ala, D-Glu, L-Glu, D-Asp, and L-Asp. Also, a comparison between two Spirulina platensis samples dried under different conditions (i.e., hot air or Iyophilized) was carried out in order to investigate the effect of the thermal processing on the amino acid content. Moreover, two procedures for the extraction of amino acids from microalgae (i.e., a classical procedure and pressurized liquid extraction (PLE)) together with different conditions for amino acid derivatization were studied in order to increase the sensitivity of the whole analytical method. By using the selected chiral-MEKC-LIF conditions (100 mM sodium tetraborate, 30 mM SDS, and 20 mM beta-CD at pH 9.7) the main microalgae D/L-aa are separated in less than 25 min with efficiencies up to 840 000 plates/m and good sensitivity (i.e., 330 ng of D-Arg per gram of microalga could be detected by this procedure for an S/N of 3). Several D-aa were detected in all the microalgae, observing interesting differences in their D/L-aa profiles, what corroborates the usefulness of the chiral-MEKC-LIF approach to characterize different microalgae species as well as different microalgae drying processes. Moreover, the use of PLE can selectively extract different free amino acids from microalgae.