Microalgae have significant potential to be an important alternative energy source, but the challenges to the commercialization of bio-oil from microalgae need to be overcome for the potential to be realized. The application of stress can be used to improve bio-oil yields from algae. Nevertheless, the understanding of stress effects is fragmented due to the lack of a suitable, direct quantitative marker for stress. The lack of understanding seems to have limited the development of stress based strategies to improve bio-oil yields, and hence the commercialization of microalgae-based bio-oil. In this study, we have proposed and used the specific intracellular reactive species levels (siROS) particularly hydroxyl and superoxide radical levels, separately, as direct, quantitative, markers for stress, irrespective of the type of stress induced. Although ROS reactions are extremely rapid, the siROS level can be assumed to be at pseudo-steady state compared to the time scales of metabolism, growth and production, and hence they can be effective stress markers at particular time points. Also, the specific intracellular (si-) hydroxyl and superoxide radical levels are easy to measure through fluorimetry. Interestingly, irrespective of the conditions employed in this study, that is, nutrient excess/limitation or different light wavelengths, the cell concentrations are correlated to the siROS levels in an inverse power law fashion. The composite plots of cell concentration (y) and siROS (x) yielded the correlations of y = k1 · x−0.7 and y = k2 · x−0.79, for si-hydroxyl and si-superoxide radical levels, respectively. The specific intracellular (si-) neutral lipid levels, which determine the bio-oil productivity, are related in a direct power law fashion to the specific hydroxyl radical levels. The composite plot of si-neutral lipid levels (z) and si-hydroxyl radical level (x) yielded a correlation of z = k3 · x0.65. More interestingly, a nutrient shift caused a significant change in the sensitivity of neutral lipid accumulation to the si-hydroxyl radical levels. Biotechnol. Bioeng. 2013; 110: 1627–1636. © 2013 Wiley Periodicals, Inc.