Snail genes comprise a family of zinc-finger transcription factor coding genes with multiple roles in early embryonic development of metazoans. The evolutionary history of this family has been studied in detail, revealing an initial duplication in Snail and Scratch genes preceding the protostome/deuterostome split, and posterior independent duplication events in the lineages leading to insects and vertebrates. The distribution of mammalian and teleost Snail genes fits with current models for whole genome duplication events at the base of the vertebrate lineage, plus an extra duplication in teleosts. However, two very divergent Snail genes, one from mammals and the other from teleost fishes, fit poorly into the phylogenetic analysis of the family. By means of database mining and synteny analysis, we provide evidence for these genes being orthologues, and evidence that they originated in an early duplication at the base of the vertebrates resulting in three and not two Snail genes. We further show that all three Snail genes lie in regions of extensive paralogy, revealing their common origin through segmental or chromosomal duplication.