To analyze the organization of planarian brain, a homolog of the homeobox-containing gene Orthopedia (Otp) from planarian, Djotp, was isolated. The homeodomain of Djotp differs from mouse Otp by only two amino acids. This conservation extends to include a 12 amino acid motif downstream of the homeodomain. Whole mount in situ hybridization studies indicated that Djotp is specifically expressed in the branch structures of the normal planarian adult brain. During regeneration, Djotp is expressed in the presumptive branch region prior to branch formation. These observations implicate a role for Djotp in establishing and maintaining the identity of the planarian brain branch region. The results suggest that recruitment of Otp for its role in brain pattern formation occurred very early in evolution.