<p>Integrating morphological, functional and molecular information of individual neurons is critical for classifying neuronal cell types and probing circuit mechanisms of brain functions. Despite the emergence of extensive single-neuronal morphology datasets largely via random sparse labeling, it remains challenging to map arbitrarily selected neuron’s morphology in vivo, especially in conjunction with its functional and molecular characteristics. Here, we report a genetically encoded Photo-inducible single-cell labeling system (Pisces) that enables simple, rapid and long-term in vivo labeling of the entire morphology of arbitrary neurons, as exemplified in intact larval zebrafish. Pisces allows sequential tracing of multiple neurons within individual animals, facilitating brain-wide projectome mapping. Importantly, combined with in vivo calcium imaging, and fluorescence in situ hybridization or single-cell RNA sequencing, Pisces allows linking individual neurons’ morphology characterization with their functional and/or gene expression investigation, respectively. This strategy promises to advance the construction of single-neuronal multimodal atlases and expedite the elucidation of neural circuitries underlying brain functions.</p>