Mitochondria are highly dynamic organelles that undergo fusion and fission on a relatively fast time scale. Here, a straightforward method is described for capturing mitochondrial fusion events in real time using a photoconvertible fluorescent protein and a far-field fluorescence microscope equipped with appropriate image acquisition and analysis software. The Kaede photoconvertible fluorescent protein is tagged with a mitochondrial targeting sequence and delivered to primary neurons by lentiviral transduction, which ensures efficient low copy number transgene insertion, as well as stable transgene expression.