Optical and genetic tools are beginning to revolutionize the studies of neuronal circuits. Neurons can now be labeled with conventional or genetically encoded indicators that allow their activity to be monitored during behavior in intact animals. Laser ablations and genetic inactivation offer ways to perturb activity of specific cells to test their contributions to behavior. These approaches promise to speed progress in the understanding of vertebrate networks in genetic model systems such as mice and zebrafish. Here we review some of the progress in applying these tools, with an emphasis on our work to develop and apply these approaches in the zebrafish model.