Amphioxus are primitive chordates that share several common anatomical features with vertebrates, such as a notochord and a dorsal nerve cord. The Brachyury (T) gene is required for notochord differentiation in vertebrates and an ascidian homologue of this gene is expressed in notochord cells at the time of developmental fate restriction. To gain insight into the molecular and developmental mechanisms underlying the evolution of chordates, we amplified a cDNA fragment for an amphioxus homologue (BbT1) of the mouse T gene, with which we examined the spatial expression of the BbT1 gene. In situ hybridization showed that BbT1 transcript was undetectable in eggs, as well as in early embryos at the cleavage and blastula stages. Distinct hybridization signals were first evident in the mesoderm of gastrulae but neither the ectoderm nor endoderm showed the signals. As development proceeded to the neurula stage, the signals became conspicuous in the primordial somite at the dorsolateral wall of the archenteron, while the primordial notochord at the dorsomedian wall of the archenteron emitted less intense hybridization signals. These results suggested that the T gene is conserved by amphioxus and that the BbT1 gene is expressed in the mesodermal region of the gastrula and neurula.