Photoactivatable fluorescent proteins (PAFPs) undergo pronounced changes in fluorescent properties by irradiation with specific light. These changes enable the spatial and temporal optical labelling and tracking of living cells, organelles and intracellular molecules. Here we introduce the characteristics of known PAFPs and their potential applications from several aspects, including molecular labelling and dynamic analysis, protein-protein interaction, organelle and cellular compartment dynamics, cell tracking, and recent use in photoactivated localization microscopy. We also discuss the use of photoactivable fluorescent protein in plant molecular cell biology.