Recent studies have demonstrated that Zfhx1a and Zfhx1b are transcription factors involved in many important signaling pathways. They are known to be essential for neural development, and for the development of other neural-crest-derived tissues. However, much remains to be learned about their expression patterns and functions in the developing tissues of the craniofacial region. We determined the unique expression patterns of Zfhx1a and Zfhx1b during mouse craniofacial development from embryonic day (E) 13.5 to E16.5. In the epithelium of the circumvallate papilla facing the oral cavity, Zfhx1a and Zfhx1b were strongly and weakly expressed, respectively. The epithelial component of the submandibular gland expressed Zfhx1a and Zfhx1b. In the developing eye, Zfhx1a and Zfhx1b were expressed strongly in the retina, and in the anterior region of the lens at E13.5 and E14.5. At E16.5, transcripts of Zfhx1a and Zfhx1b were detected in the developing eyelids. These findings demonstrate the spatial and temporal expression patterns of Zfhx1a and Zfhx1b during mouse craniofacial development.