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The aim of this study was to optimize and to propose the suitable separation method and storage conditions for specific species of microalgae. The performance of different separation methods for the recovery of cell biomass of marine microalgae, Chaetoceros calcitrans, from the culture broth was evaluated. The microalgae were cultivated using 10 L photobioreactor. The microalgae cell cultures were concentrated either by centrifugation, tangential flow filtration or flocculation and then stored at different temperatures (-20, 4 and 27°C) to investigate the optimum storage conditions for C. calcitrans prior to different downstream processing methods. High concentration of cell in slurry (4.88x107 cells mL-1) was obtained using centrifugation as compared to tangential flow filtration (4.14x107 cells mL-1), flocculation with chitosan (1.56x107 cells mL-1) and flocculation with Magnafloc®LT 25 (8.24x106 cells mL-1). Storage of C. calcitrans biomass at chilled temperature (4°C) directly after the harvesting using these four different separation methods resulted in extended shelf life (> 4 weeks). Frozen biomass (-20°C) fails to preserve the quality of C. calcitrans after they were revived in fresh medium. C. calcitrans flocculated with 0.5 mg L-1 Magnafloc®LT 25 was able to maintain the quality of the cells after storage at 27°C for more than 2 weeks. However, flocculation of cells with 20 mg L-1 chitosan, centrifugation at 8000 rpm for 10 min and tangential flow filtration process at transmembrane pressure of 20 psi failed to retain the quality of biomass after storage for 2 weeks at 27°C.