Oleaginous microorganisms, such as yeast, fungi, microalgae and bacteria, represent a key segment of second generation feed-stock materials and are considered to synthesize a wide range of industrially important chemical compounds. Oleaginous microorganisms possess a broad varieties of chemical compounds such as carotenoids, pigments, carbohydrates, chlorophyll, and storage-material lipids. Oleaginous microorganisms have been recognized as promising sources for the synthesis of unsaturated, especially polyunsaturated fatty acids (PUFA). So far, a variety of high-throughput screening methodologies (HTMs) have been employed for the development of bioprocessing of oleaginous microorganisms for sustainable production of industrially valuable compounds. Of HTMs, flow cytometry (FC) and sorters (FACS) have received substantial interest as better HTMs because of their ability to screen large numbers of cells within seconds, and interrogate and isolate living cells at single-cell level. Forward and side scattering signals of FC are used to determine the physiological state of the cell while different channels available in the FC facilitate the detection of signals produced from fluorophores. Simultaneous measurement of physiological characteristics along with specific compound accumulation at single-cell level enables the possibility of separating a particular phenotype with specific properties from a population. Different microbial strain development strategies in combination with FACS produced improved phenotypes with desired properties. This review first summarizes the FACS methodologies suitable for oleaginous microorganisms and the significant progress that has been achieved in oleaginous microorganisms using FACS, and highlights the important, advanced and future prospects of FACS methodologies that are suitable for the development of bioprocessing in oleaginous microorganisms. (c) 2018 Society of Chemical Industry