An Xlox homologue gene (AtXlox) was identified in the starfish Archaster typicus. The gene consists of two exons, and encodes a polypeptide containing 228 amino acids. Although AtXlox shared 54.6 and 50.3% global amino acid sequence similarity with sea urchin SpXlox and Xenopus XlHhox8, respectively, the homeodomain of AtXlox was highly conserved. Amino acid sequence identity as high as 85 to 100% was identified between the AtXlox homeodomain and its homologues from various vertebrate and invertebrate organisms. In addition, a conserved histidine residue located at position 44 of the homeodomain of all known Xlox homologues was also identified. Results of a phylogenetic analysis based on the 60 amino acid sequence of the homeodomain indicated that AtXlox was closely related to sea urchin SpXlox. Temporal developmental mRNA expression pattern analyzed by reverse transcription (RT)-polymerase chain reaction (PCR) showed that AtXlox mRNA was mainly expressed in the early gastrula stage embryos. Whole-mount in situ hybridization revealed a ubiquitous mRNA expression pattern in archenterons as well as in ectodermal cells near the vegetal region of early and mid-gastrula stage embryos. This spatial expression pattern is very different from those of Xlox homologues in the leech, amphioxus, and in various vertebrate organisms with spatially restricted mRNA expression patterns in endodermal cells.