Development of the craniofacial skeleton is dependent on complex cellular processes involving cellular migration, differentiation and morphogenesis. Disruption of these processes can result in craniofacial defects which have a significant impact on quality of life. To identify the genes and molecular pathways involved in craniofacial development, an N-ethyl-N-nitrosourea mutagenesis forward genetic screen was performed in zebrafish. From this screen, a novel zebrafish line with craniofacial defects was discovered, which contained a mutation in the PRDM5 gene. Interestingly, PRDM5 mutations have been identified in humans with Brittle Cornea syndrome, where patients exhibit corneal thinning and severe corneal ruptures with associated hearing loss. Alcian blue staining of this unique zebrafish line revealed chondrocyte stacking defects and a morphogenic change in Meckel’s and palatoquadrate cartilage of the lower jaw. As chondrocytes are a Neural Crest derivative, these cartilage defects suggest a role for PRDM5 in Neural Crest cell development. Comparative expression analysis revealed no significant changes in Neural Crest induction and migration, however a reduction in Collagen Type 2 alpha 1 (Col2a1) was identified in homozygous mutants, suggesting that PRDM5 normally acts as a positive regulator of Col2a1 expression in cartilage precursors. Given the homology between the proximal portion of Meckel’s cartilage and the palatoquadrate cartilage of zebrafish with the incus and malleus of the middle ear in mammals, this data provides new insight into the mechanisms by which PRDM5 mutations contribute to the etiology of Brittle Cornea syndrome.