Separating specific cell phenotypes from a heterotypic mixture is a critical step in many research projects. Traditional methods usually require a large sample volume and a complex preparation process that may alter cell property during the sorting process. Here we present the use of electrical impedance as an indicator of cell health and for identifying specific microalgal phenotypes. We developed a microfluidic platform for measuring electrical impedance at different frequencies using the bacterium-sized green alga Picochlorum SE3. The cells were cultured under different salinity conditions and sampled at four different time points. Our results demonstrate the utility of electrical impedance as an indicator of cell phenotype by providing results that are consistent with known changes in cell size and physiology. Outliers in the cell data distribution are particularly useful because they represent phenotypes that have the ability to maintain size and/or membrane ionic permeability under prolonged salt stress. This suggests that our device can be used to identify and sort desired (e.g., experimentally evolved, mutant) cell phenotypes based on their electrical impedance properties.