The performance of microwaves irradiation (MAE and VMAE) to extract pigments from two marine microalgae was compared to conventional processes (cold and hot soaking and ultrasound-assisted extraction). Pigments were quantified by RP-HPLC and extraction performance was assessed regarding rapidity, reproducibility and extraction yields. Scanning electron microscopy was used at all extraction steps to assess the impact of the process on microalgal cell integrity. Freeze-drying and pigments extraction preserved microalgae cell integrity (except sonication) and evoked agglutination in superposed cells layers. All processes performed on Dunaliella tertiolecta (chlorophyte) lead to rapid pigments extraction, and equivalent pigments extraction yields, the absence of frustule allowing immediate solvent penetration in microalgae cells. In contrast, presence of the frustule in the diatom Cylindrotheca closterium (bacillariophyte) constituted a mechanical barrier to pigment extraction. MAE was identified as the best extraction process for CC pigments as it combined rapidity, reproducibility, homogeneous heating and high extraction yields. (C) 2010 Elsevier Ltd. All rights reserved.