Microalgae constitute an abundant source of poly-unsaturated fatty acids which are applied in various biotechnological fields such as pharmaceuticals and food supplement. Separating microalgae cells with respect to their lipid content would establish a relevant at-line analytical technique. The present study demonstrates an electrical approach for the separation of the lipid-producing microalgae Crypthecodinium cohnii using the effect of dielectrophoresis (DEP) in a microfluidic flow cell. Microalgae were cultivated for 8 days, while cell growth was characterized by optical density, dry cell weight, glucose concentration and lipid content via fluorescence microscopy. The size distribution of cells during cultivation was thoroughly investigated, since the DEP force scales with cell volume, but also depends on lipid content via cell electrophysiological constants. Thus, the challenge was to deconvolute one separation effect from the other, while the electrical cell constants of C. cohnii are not known yet. The DEP-dependent separation was realized by slanted top-bottom electrodes with the flowing cell suspension between them. Turning on the voltage deflected the cells from their initial path as determined by the streaming and thus changed their direction of flow. The separation efficiency of DEP was tested for various electrical field strengths and its performance was determined by quantitative analysis of optical and fluorescence videos. It could be shown for all size groups that the most lipid-containing cells were always subject to DEP separation and that the method is thus not only suitable for process analysis, but also for strain selection of the most productive cell lines.