Intercellular interactions within the branchial arch (BA) system is essential for craniofacial development. Endothelin-1 (ET-1), produced by the branchial epithelium and core mesenchyme, acts on cranial neural crest-derived ectomesenchymcal cells expressing endothelin A receptor (ETAR) and regulates expression of crucial genes such as Dlx6, a member of distalless homeobox gene family, and its downstream target dHAND, a basic helix-loop-helix transcription factor. To investigate the role of ET-1 and subsequent signaling cascades in BA development, we examined when and how they activate dHAND and Dlx6 expression. ETAR blockade by BQ123 in mouse embryo culture has revealed that ET-1/ETAR signaling is critical for dHAND and Dlx6 expression in the mandibular arch mesenchyme around embryonic day (E)8.75-E9.0 and becomes dispensable by E9.5. dHAND and Dlx6 expression after E9.5 was dependent on the presence of the epithelium, which was partly mediated by FGF-like signals. These findings indicate that ET-1/ETAR and subsequent epithelial signals are sequentially involved in BA development by maintaining dHAND and Dlx6 expression. Furthermore, discordance of dHAND and Dlx6 expression domains and heterogeneity with respect to dependency on ET-1 and FGF-like signals suggest that genetic hierarchy involving Dlx6 and dHAND is differently controlled among subdomains within the mandibular arch.