Microalgae have been proposed as carbon-neutral and sustainable fuel feedstock producers due to their fast growth and high lipid content. In this investigation, we examined the effect of different nutrient stresses on overall lipid productivities and physiology, in two microalgae species, namely Nannochloropsis sauna and Dunaliella saline. For both the species in semi-continuous cultures, the dilution ratio was found to affect only the harvest period and not the biomass or lipid productivity. Harvest at different growth phases was influenced by the temporal nutrient status of the medium leading to different productivity of biomass and lipids. These two species also showed different cellular biochemistry and lipid metabolism in response to the different nutrient stresses. More efficient stimulators of lipid production than the commonly employed nitrogen limitation were identified, for e.g. deficiency of trace element. Significant influence of nutrient deficiency on lipid profiles was observed in N. sauna, such as chain length and degree of unsaturation, with desirable characteristics for biodiesel production. The comparison of lipid profiles between these two species revealed phenomenal differences in some fatty acids, e.g. a higher level of gamma-linolenic acid (C18:3n6) in D. sauna and the exclusive presence of palmitoleic acid in N. saline. The biochemical composition with respect to the cellular function of the fatty acids is discussed with an attempt to better understand the differences in the lipid profiles. (C) 2015 Elsevier Ltd. All rights reserved.