Learning how to actively avoid a predictable aversive stimulus involves two steps: recognizing the cue that predicts upcoming punishment, and learning a behavioral response that will lead to avoidance. In zebrafish, ventral habenula (vHb) neurons have been proposed to participate in both steps by encoding the expected aversiveness of a stimulus. vHb neurons increase their firing rate as expectation of punishment grows, but reduce their activity as avoidance learning occurs. How the change in vHb activity occurs is not known. Here, we ask whether the neuromodulator kisspeptin1, which is expressed in the ventral habenula, could be involved. Kiss1 mutants were generated with Cas9 using guide RNAs targeted to the signal sequence. Mutants, which have a stop codon upstream of the kisspeptin1 peptide, have a deficiency in learning to avoid a shock that is predicted by light. Electrophysiology indicates that kisspeptin1 has a concentration-dependent effect on vHb neurons: depolarizing at low concentrations and hyperpolarizing at high concentrations. These data suggest that as the fish learns to cope with a threat, kisspeptin1 may differentially modulate vHb neurons. This implies that learning a behavioral strategy to overcome a stressor is accompanied by physiological change in habenula neurons.