Localization of mRNAs plays pivotal roles in different cell types, including neurons and the cells in the developing stages. To visualize the dynamic movements of mRNAs in living cells, many methods have been emerged in the past decade. However, it has not been realized to visualize endogenous mRNAs with genetically encoded fluorescent probes. We recently developed fluorescent protein-based RNA probes for characterizing the localization and dynamics of mRNAs in single living cells. The probes consist of two RNA-binding domains of human PUMILIO1, each connected with split fragments of a fluorescent protein capable of reconstitution upon binding to a target mRNA. The probes are modified to specifically recognize a 16-base sequence of an mRNA of interest and to target into organelles by means of a short signal peptide. We have shown that ND6 mRNA is concentrated particularly on mitochondrial DNA (mtDNA) and movement of the mRNA is restricted in mitochondria. The probes provide a general means to study spatial and temporal mRNA localization and dynamics in intracellular compartments in living cells.