Morphological innovations like the acquisition of the neural crest as well as gene family expansions by genome duplication are considered as major leaps in the evolution of the vertebrate lineage. Using comparative genomic analyses, we have reconstructed the evolutionary history of the endothelin system, a signaling pathway consisting of endothelin ligands and their G protein-coupled receptors. The endothelin system plays a key role in cardiovascular regulation as well as in the development of diverse neural crest derivatives like pigment cells and craniofacial bone structures, which are hot spots of diversity in vertebrates. However, little is known about the origin and evolution of the endothelin system in the vertebrate lineage. We show that the endothelin core system, that is, endothelin ligands (Edn) and their receptors (Ednr), is a vertebrate-specific innovation. The components of the endothelin core system in modern vertebrate genomes date back to single genes that have been duplicated during whole-genome duplication events. After two rounds of genome duplication during early vertebrate evolution, the endothelin system of an ancestral gnathostome consisted of four ligand and four receptor genes. The previously unknown fourth endothelin ligand Edn4 has been kept in teleost fish but lost in tetrapods. Bony vertebrates generally possess three receptor genes, EdnrA, EdnrB1, and EdnrB2. EdnrB2 has been lost secondarily in the mammalian lineage from a chromosome that gave rise to the sex chromosomes in therians (marsupials and placentals). The endothelin system of fishes was further expanded by a fish-specific genome duplication and duplicated edn2, edn3, ednrA, and ednrB1 genes have been retained in teleost fishes. Functional divergence analyses suppose that following each round of genome duplication, coevolution of ligands and their binding regions in the receptors has occurred, adjusting the endothelin signaling system to the increase of possible ligand-receptor interactions. Furthermore, duplications of genes involved in the endothelin system are associated with functional specialization for the development of particular neural crest derivatives. Our results support an important role for newly emerging ligands and receptors as components of signaling pathways and their expansion through genome duplications in the evolution of the vertebrate neural crest.