The phenotypic diversity found in vertebrates is closely related to modifications in the transcription patterns of developmental genes. Developmental genes often participate in several patterning processes and are thus very well conserved. In contrast, their associated cis-regulatory elements (CREs) function in a mostly time and tissue specific manner. Genetic modifications within CREs may thus alter the pattern of expression of their target developmental gene in a spatiotemporal limited manner. Consequently, they may lead to morphological changes with less probability of associated lethality than mutations affecting coding sequences. For this reason, understanding the mechanisms of CREs evolution is key to gain insight into vertebrate diversification.