Retinoic acid regulates development of many chordate-specific characteristics. The genes encoding retinoic acid receptors (RARs) were isolated only from chordates. In the present study, a genomic DNA fragment containing the promoter region of the RAR gene (Ci-RAR) in the protochordate Ciona intestinalis was isolated. The transgene containing 1,326 bp of the Ci-RAR 5' flanking region was expressed in the epidermis, central nervous system, and muscle. The sequence element necessary for expression in the epidermis seemed to be subdivided into two elements. One was required for activation in the dorsal midline epidermis and the other for the rest of the epidermis. The element responsible for activation in the central nervous system was characterized by putative binding sites for Fox, Ets, and GATA transcription factors. An E-box sequence was required for the transgene expression in the tail muscle cells.