Nitric oxide synthase catalyzes the production of nitric oxide, a multifunctional signaling molecule that affects diverse aspects of animal physiology such as cell proliferation, differentiation, neurotransmission and apoptosis. Here, we report the cloning and expression pattern of the zebrafish nnos. This gene was mapped to zebrafish linkage group 5. The spatial and temporal expression pattern of nnos in embryonic zebrafish was analyzed by whole mount in situ hybridization. nnos is widely expressed in the embryonic nervous system. Expression of zebrafish nnos appeared at 16 hours post-fertilization in the hypothalamus and by 3 days post-fertilization was present in discrete locations in the central nervous system as well as the enteric nervous system. Some nnos-positive cells were mapped to specific locations in the central nervous system using tyrosine hydroxylase as a specific marker indicating that nnos transcripts were present in the olfactory bulb, anterior diencephalon, posterior hypothalamus and anterior hindbrain.