Autophagy contributes to various cellular processes, including innate immunity, development, and programmed cell death (PCD) in multicellular organisms. In plants, autophagy plays roles in recycling of proteins and metabolites including lipids, and is involved in many physiological processes, such as abiotic and biotic stress responses. Furthermore, rice mutants defective in autophagy showed sporophytic male sterility and reduced accumulation of lipids and starch in pollen grains at the flowering stage and exhibited reduced pollen germination activity, indicating crucial roles of autophagy during plant reproductive development. An in vivo imaging system has been established to analyze the dynamics of autophagy in rice as well as in cultured tobacco cells using GFP-ATG8, a marker of autophagosomes. In the present study, we review the spatiotemporal dynamics of autophagic fluxes in plant cells and discuss their possible significance in PCD and metabolic regulation, with particular focus on plant reproductive development.