Evolutionary model systems have emerged as a rich source of natural genotypic and phenotypic variation, from which we can characterize the genetic architecture underlying morphological features. The Mexican tetra (Astyanax mexicanus), inclusive of interfertile river (surface)- and cave-dwelling morphs, provides a powerful comparative paradigm to study the genetic basis of a variety of traits evolving under extreme environmental pressures. Cavefish harbor numerous craniofacial differences compared to their surface-dwelling counterparts, including an elongated lower jaw (underbite) and an increase in the number of teeth. In order to investigate genes underlying orofacial traits, we performed Quantitative Trait Loci (QTL) analysis across individuals from an F₂ hybrid pedigree. We discovered significant QTL for bite, tooth size, and tooth number. An underbite, decrease in upper jaw tooth size and increase in tooth number are all associated with the homozygous cavefish genotype. We further explored candidate genes associated with significant QTL regions using BLAST and GO terms analyses. To understand why these changes evolved in cavefish, we performed feeding behavior assays in hybrids with both underbite and overbite phenotypes. Taken together, this work provides novel insight into the genetic regulators of facial bone and tooth development in the context of trait evolution.