The salamander axolotl (Ambyostoma mexicanum) is a model for studying nervous system evolution, development, and regeneration. Axolotls can regenerate injuries to the central and peripheral nervous system making them an ideal model to study formation and regeneration of neuronal circuits. Tools to visualize and manipulate cells of the axolotl nervous system with high efficiency, spatial and temporal precision are therefore greatly required. Recombinant adeno-associated viruses (AAVs) are frequently used for in vivo gene transfer of the nervous system but virus-mediated gene delivery to the axolotl nervous system had not yet been described. Here, we demonstrate the use of AAVs for efficient gene transfer within the axolotl brain and the retina. We show that serotypes AAV8, AAV9, AAVRG and AAVPHP.eB are suitable viral vectors to infect both excitatory and inhibitory neuronal populations of the axolotl brain. We further use AAV9 to trace retrograde and anterograde projections between the retina and the brain and determine the existence of a retinopetal cell population in the axolotl. Together, our work establishes AAVs as a powerful tool to interrogate neuronal circuit organization in the axolotl.