The faces of birds and mammals exhibit remarkable morphologic diversity, but how variation arises is not well-understood. We have previously demonstrated that a region of facial ectoderm, which we named the frontonasal ectodermal zone (FEZ), regulates proximo-distal extension and dorso-ventral polarity of the upper jaw in birds. In this work, we examined the equivalent ectoderm in murine embryos and determined that the FEZ is conserved in mice. However, our results revealed that fundamental differences in the organization and constituents of the FEZ in mice and chicks may underlie the distinct growth characteristics that distinguish mammalian and avian embryos during the earliest stages of development. Finally, current models suggest that neural crest cells regulate size and shape of the upper jaw, and that signaling by Bone morphogenetic proteins (Bmps) within avian neural crest helps direct this process. Here we show that Bmp expression patterns in neural crest cells are regulated in part by signals from the FEZ. The results of our work reconcile how a conserved signaling center that patterns growth of developing face may generate morphologic diversity among different animals. Subtle changes in the organization of gene expression patterns in the FEZ could underlie morphologic variation observed among and within species, and at extremes, variation could produce disease phenotypes.