The unique combination of small size, translucent brain, and powerful genetics makes zebrafish an ideal vertebrate model system to investigate normal and pathological brain functions. However, it remains challenging to map out the myriad of connections between neurons and identify cellular level connectivity changes during development or disease. We recently found that vesicular stomatitis virus (VSV) can effectively infect zebrafish neurons and label connected neurons, paving the way for rapid brain mapping (J Comp Neurol. 2015; 523:1639-63). In this study, we combined multiple types of recombinant transsynaptic VSV, neurotransmitter phenotyping, and semi-automated 3D brain mapping to analyze the connectivity patterns between the retina and the brain in wild-type and mutant zebrafish. In wild-type fish, we observed VSV labeled retinorecipient cells near the visual afferent terminals in the diencephalon and the optic tectum, consistent with previous studies. Next, we analyzed zebrafish mutants of dscaml1, a conserved neuronal transmembrane molecule implicated in human autism spectrum disorder. dscaml1 homozygous mutants show greatly reduced connections, and the decrease is non-uniform among different brain regions. The reduced connectivity to the optic tectum, a critical region for saccade generation, may contribute to the reduced saccadic eye movements observed in mutants. Together, these results suggest novel roles for dscaml1 in establishing neuronal connectivity and visual behaviors. This approach will likely be useful for neuronal connectivity analysis in other zebrafish mutants or disease models.