SUMMARY Amphioxus and vertebrates are the only deuterostomes to exhibit unequivocal somitic segmentation. The relative simplicity of the amphioxus genome makes it a favorable organism for elucidating the basic genetic network required for chordate somite development. Here we describe the developmental expression of the somite marker, AmphiTbx15/18/22, which is first expressed at the mid-gastrula stage in dorsolateral mesendoderm. At the early neurula stage, expression is detected in the first three pairs of developing somites. By the mid-neurula stage, expression is downregulated in anterior somites, and only detected in the penultimate somite primordia. In early larvae, the gene is expressed in nascent somites before they pinch off from the posterior archenteron (tail bud). Integrating functional, phylogenetic and expression data from a variety of triploblast organisms, we have reconstructed the evolutionary history of the Tbx15/18/22 subfamily. This analysis suggests that the Tbx15/18/22 gene may have played a role in patterning somites in the last common ancestor of all chordates, a role that was later conserved by its descendents following gene duplications within the vertebrate lineage. Furthermore, the comparison of expression domains within this gene subfamily reveals similarities in the genetic bases of trunk and cranial mesoderm segmentation. This lends support to the hypothesis that the vertebrate head evolved from an ancestor possessing segmented cranial mesoderm.