The plant secretory and endocytic pathways consist of several functionally distinct membrane-bounded compartments. The ultra structures of the endoplasmic reticulum, the Golgi apparatus, and central vacuoles have been well characterized via traditional structural electron microscope (EM). However, the identification of plant prevacuolar compartments (PVCs) and early endosomes (EEs) had not been achieved until more recently because of the lack of specific markers for these organelles. Recent development of fluorescent reporters for PVCs and EEs expressing in transgenic tobacco BY-2 cells and Arabidopsis plants has allowed their dynamic characterization in living cells via confocal microscopy and drug treatment, which led to their subsequent morphological identification via structural and immunogold EM. Thus, In this review, we will use our studies on PVCs and EEs as examples to present an efficient approach for organelle identification in plant cells via primary characterization of fluorescent-marked organelles In living cells and their dynamic response to drug treatments, which then serves as the basis for subsequent immunogold and structural EM studies for organelle identification. Such strategy thus represents a powerful approach in future research for the identification of novel organelles and transport vesicles in plant cells.