We have identified an amphioxus T-box gene that is orthologous to the Eomesodermin, T-brain-1, and Tbx21 genes of vertebrates, and we have characterized its expression pattern during embryonic and larval development. AmphiEomes/Tbr1/Tbx21 is maternally expressed in oocytes and cleavage stage embryos. After the onset of zygotic transcription at the blastula stage, it is expressed in invaginating mesendoderm cells during gastrulation, but it is downregulated in presumptive ectoderm and neurectoderm. Expression is seen in both axial and paraxial mesendoderm in neurulae and early larvae, but it is not detected in differentiated endoderm, somites, or notochord. Expression persists in mesendoderm cells of the tail bud in early larvae, but it disappears between 1 to 1.5 days post fertilization. Unlike orthologous genes in basal deuterostomes or vertebrates, no anterior neural expression domain is detected at any stage of development. Integrating phylogenetic and developmental data, we have reconstructed the evolutionary history of the Eomesodermin/Tbr1/Tbx21 subfamily of T-box genes from a single ancestral locus that originated very early in metazoan evolution, before the evolution of triploblasts from their diploblast ancestor.