Mitochondria trafficking plays an essential role for supplying energy in the neuronal system. We report here a red emissive two-photon probe for mitochondria (CMT-red) that showed high selectivity and robust staining ability for mitochondria, high photostability under a two-photon microscopy imaging condition, and low cytotoxicity. This probe can be easily loaded into live cells and tissue and used for real-time, high resolution imaging of the mitochondria trafficking in primary cortical neurons as well as in rat hippocampal tissue.