Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO
in vivo
, is substantial, the origin of a large and diversified repertoire of
nos
gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of
nos3
in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore
nos
gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first,
nos2
experienced several lineage-specific gene duplications and losses. Second,
nos3
was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one
nos
paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that
nos
expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on
nos
genes’ roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.