Transmission electron, confocal microscopy and FACS in conjunction with two different lipophilic fluorescent dyes, BODIPY 505/515 and Nile Red were used to describe the cellular development and lipid bodies formation in Aurantiochytrium sp. KRS101. TEM results revealed that multi-cellular spores were appeared in sporangium during early-exponential phase, and spores were matured in mid-exponential phase followed by release of spores from sporangium in late-exponential phase. TEM and FACS analyses proved that lipid bodies appeared, developed and degenerated in mid-exponential, early- and late-stationary phases, respectively. The staining results in FACS indicate that BODIPY 505/515 is more effective for the vital staining of intracellular lipid bodies than Nile Red. FACS based single cell sorting also showed healthy growth for BODIPY 505/515 stained cells than Nile Red stained cells. In addition, a quantitative baseline was established either for cell growth and/or lipid accumulation based on cell count, fatty acid contents/composition, and sectional/confocal images of KRS101.