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Salinity fluctuation is an important factor affecting outdoor microalgae culture. This investigation examined the effect of salinity change (Tr-1:35–15 g/L, Tr-2:35–25 g/L, Tr-3:35–35 g/L, Tr-4:35–45 g/L, and Tr-5:35–55 g/L) on growth and the biochemical composition of Nannochloropsis oculata, a candidate for biodiesel production in indoor photo-bioreactors. Results showed that the algae increased in absorbency and dry biomass as salinity decreased. When the salinity increased, the specific growth rate (SGR) of the algae decreased significantly. The salinity stress also affected the pigments of the algae, the chlorophyll-a, and carotenoid contents of the algae which decreased with the increase of salinity from 45 to 55 g/L. The fatty acid methyl esters (FAME) content (% of dry biomass) increased with the increase of salinity (e.g., Tr-4 and Tr-5). The algae was rich in C16:0 (palmitic acid), C16:1n-7 (palmitoleic acid), and C20:5n-3 (eicosapentaenoic acid), and C16:0 content increased with decreasing salinity from 35 to 15 g/L, but C16:1n-7 content was high in all the treatments ranging from 25.25 ± 1.42% in Tr-1 to 27.05 ± 1.13% in Tr-5.