To date, on line monitoring in bioprocesses is restricted to conventional parameters. Presently, advances in microscopy allow the monitoring of single-cell size distributions in a bypass or in situ. These data provide information regarding population heterogeneity, substrate conversion, or product synthesis as these parameters are related to the size of the cells. In this study, changes in the single-cell size distribution of the heterotrophic microalgae Crypthecodinium cohnii were tracked with holographic microscopy and a photo-optical microscopy probe, which is applicable in situ. This algae produces the polyunsaturated fatty acid docosahexaenoic acid (DHA). On the basis of the cell size and broadness of the size distribution, the applied methods enabled to distinguish between cells in the growth and production phase. Under conditions of low growth and high fatty acid accumulation, the cell size kept concomitantly changing. The correlation between cell size measurements and the intracellular DHA content was confirmed by regression analysis. The phase heterogeneity, which was measured by holographic microscopy, changed simultaneously with the DHA synthesis. The amount of information obtained by both digital holographic and in situ microscopy is similar to that obtained by flow cytometry but with reduced effort for a real-time analysis. (C) 2016 Elsevier Ltd. All rights reserved.