Amphibians hold a unique position in the study of the evolution and development of the vertebrate the central nervous system (CNS), as they reflect the transition from aquatic to land-based locomotion. A comprehensive exploration of the amphibian CNS, however, necessitates genetic and neural tracing tools, which were previously limited.Adeno-associated viruses (AAVs) have gained popularity in mammals, due to lack of toxicity and host genome integration. Aiming to add AAVs to the amphibian toolkit, we tested AAV serotypes for CNS transduction in three distantly-related amphibian species: the frogs Xenopus laevis and Pelophylax bedriagae, and the salamander Pleurodeles waltl.Our comprehensive screen identified efficient neurotropic anterograde or retrograde serotypes for each species. AAV-mediated tracing of the amphibian pallium identified confirmed and novel forebrain circuits. In Xenopus, we mapped contralateral pallial connections, previously only described in distantly-related frog species. In Pleurodeles, we revealed novel tecto-pallial projections. Establishment of amphibian AAV tracers therefore enables further dissection of circuit transformation and evolution. Additionally, we demonstrated the ability of AAVs to target isochronic cohorts in premetamorphic amphibians. We tracked pallium, optic tectum and spinal cord formation, enabling cross-species comparisons of developmental progression. Results suggest sequential formation of cortical layers and dorso-ventral spinal cord expansion.Combined, these findings introduce AAVs to amphibian neuroscience research and solidify their status as a neuron labeling and manipulation tool with broader applicability across vertebrate species. The ability of AAVs to target neuronal subsets by input-output connectivity or developmental time facilitates the evaluation of their conservation, origin and ultimately, function.