Development of the mammalian face requires a large number of genes that are expressed with spatio-temporal specificity, and transcriptional regulation mediated by enhancers plays a key role in the precise control of gene expression. Using chromatin immunoprecipitation for a histone marker of active enhancers, we generated a genome-wide map of candidate enhancers from the maxillary arch (primordium for the upper jaw) of mouse embryos. Furthermore, we confirmed multiple novel craniofacial enhancers near the genes implicated in human palate defects through functional assays. We characterized in detail one of the enhancers (Lhx8_enh1) located upstream of Lhx8, a key regulatory gene for craniofacial development. Lhx8_enh1 contained an evolutionarily conserved binding site for Lymphoid Enhancer Factor (LEF)/T-Cell Factor (TCF) family proteins, which mediate the transcriptional regulation by WNT/β- catenin signaling pathway. We demonstrated in vitro that WNT/β-catenin signaling was indeed essential for the expression of Lhx8 in the maxillary arch cells, and that Lhx8_enh1 was a direct target of WNT/β-catenin pathway. Together, we uncovered a molecular mechanism for the regulation of Lhx8, and provided valuable resources for further investigation into the gene regulatory network of craniofacial development.