Visualizing neuronal mitochondria in a living, intact mammalian organism is a challenge that can be overcome in zebrafish larvae, which are highly accessible for optical imaging and genetic manipulation. Here, we detail an approach to visualize neuronal mitochondria in sensory Rohon–Beard axons, which allows quantitatively measuring mitochondrial shape, dynamics, and transport in vivo. This provides a useful assay for basic studies exploring the behavior of neuronal mitochondria in their natural habitat, for revealing the influence that disease-related alterations have on this behavior and for testing pharmacological compounds and genetic manipulations that might ameliorate disease-related mitochondrial phenotypes in neurons.