Fluorescent probes are a powerful tool for visualizing cellular and subcellular structures, their dynamics, and cellular molecules in living cells, and enables us to monitor cellular processes in a spatio-temporal manner within complex and crowded systems. In addition to popular fluorescent proteins, a wide variety of small-molecule dyes have been synthesized through close association with the interdisciplinary field of chemistry and biology, ranging from those suitable for labeling cellular compartments such as organelles to those for labeling intracellular biochemical and biophysical processes and signaling. In recent years, self-labeling technologies including the SNAP-tag system have allowed us to attach these dyes to cellular domains or specific proteins, and are beginning to be employed in plant studies. In this mini review, we will discuss the current range of synthetic fluorescent probes that have been exploited for live cell imaging and the recent advances in the application that enable genetical tagging of synthetic probes in plant research.