Animals control motor actions at multiple timescales. We use larval zebrafish and advanced optical microscopy to understand the underlying neural mechanisms. First, we examined the mechanisms of short-term motor learning by using whole-brain neural activity imaging. We found that the 5-HT system integrates the sensory outcome of actions and determines future motor patterns. Second, we established a method for recording spiking activity and membrane potential from a population of neurons during behavior. We identified putative motor command signals and internal copy signals that encode millisecond-scale details of the swimming dynamics. These results demonstrate that zebrafish provide a holistic and mechanistic understanding of the neural basis of motor control in vertebrate brains.