We previously characterized the arginine vasotocin receptor sequences in the jawless vertebrate sea lamprey. These gene and protein sequences provide clues to the origins of the various arginine vasopressin and oxytocin receptor family members in jawed vertebrates. However, orthological relationships between the jawless and jawed receptors is unclear. The current work is a closer examination and comparison between these G protein-coupled receptor sequences of the lamprey, the early jawed vertebrate elephant shark, and the boned fish and tetrapods. Our objective was to gain more insight into the differentiation of key signaling domains, which may then aid in discerning the pattern and timing of whole genome duplication early in the vertebrate lineage. The lamprey receptors remain less differentiated than shark receptors, due in part to the single vasotocin ligand in the lamprey and the selection pressure of a second ligand, oxytocin, in the shark. However, variation in G proteins utilized among the V1A, V1B and oxytocin receptor types has also contributed to differentiation, as well as leading to a change in second-messenger signaling pathway in the V2-type receptors. Conservation of gene regulatory elements may provide additional evidence of receptor gene orthology. These molecular evolution studies can ultimately be informative in applications such as drug discovery and environmental toxicology to determine cross-species sensitivity to chemicals.