Quantifying regulatory gene effects on dental morphology and function has implications for the underlying mechanisms that generated dental diversity in mammals. We tested the hypothesis that regulatory gene expression changes lead to differences in molars using a neural crest knockout of bone morphogenetic protein 7 (BMP7) in Mus musculus. 3D geometric morphometric methods were used to quantify the shape of the molar toothrow. BMP7 mutants have extra cusps on the first upper and lower molars, and alterations in cusp orientation and morphology. Further, significant shape differences between control and mutant were found for upper and lower toothrows. Mutant mice also exhibited differences in attrition facets, indicating functional changes that could lead to advantages chewing new food resources and eventually niche diversification. The size ratio of the molars in the toothrow remained unchanged, implying that BMP7 induced changes in molar size ratio are a result of knocking out epithelial, rather than neural crest, expression of BMP7. Our results indicate that changes in BMP7 expression are sufficient to alter morphology and function of the toothrow, suggesting that BMP7 or genes affecting its function could have played a role in structuring the dental diversity of extinct and extant mammals.