Background: Fetal Alcohol Spectrum Disorders (FASD) describe a continuum of ethanol-induced developmental defects including commonly observed craniofacial malformations. While ethanol-sensitive genetic mutations are a major contributor to facial malformations, the impacted cellular mechanisms underlying these facial anomalies remain unknown. The Bone Morphogenetic Protein (Bmp) signaling pathway is a key regulator of epithelial morphogenesis driving facial development, providing a possible ethanol-sensitive mechanism to malformations to the facial skeleton. Methods: Using zebrafish, we tested several mutants for Bmp pathway components for ethanol-induced facial malformations. Mutant embryos were exposed to ethanol in the media from 10-18 hours post-fertilization (hpf). Exposed zebrafish were fixed at 36 hpf to analyze anterior pharyngeal endoderm size and shape by immunofluorescence or at 5 days post-fertilization (dpf) to quantitatively examine shape of the facial skeleton stained with Alcian Blue/Alizarin Red staining. Integrating human genetic data, we screened for Bmp-ethanol associations in jaw volume of ethanol-exposed children. Results: We found that mutations in the Bmp pathway sensitize zebrafish embryos to ethanol-induced malformations to anterior pharyngeal endoderm shape, leading to altered expression of fgf8a in the oral ectoderm. These changes correlate with shape changes in the viscerocranium, suggesting that ethanol-induced malformations of the anterior pharyngeal endoderm lead to facial malformations. Variants in the Bmp receptor gene, BMPR1B were associated with ethanol-related differences in jaw volume in humans. Conclusions: For the first time, we show that ethanol exposure disrupts proper morphogenesis of, and tissue interactions between, the facial epithelia. These shape changes in the anterior pharyngeal endoderm-oral ectoderm-signaling axis during early zebrafish development mirror the overall shape changes observed in the viscerocranium and were predictive for Bmp-ethanol associations in jaw development in human. Collectively, our work provides a mechanistic paradigm linking the impact of ethanol to the epithelial cell behaviors that underlie facial defects in FASD.