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ABSTRACT The regulation of bone size is a poorly understood and complex developmental process. Evolutionary models can enable insight through interrogation of the developmental and molecular underpinnings of natural variation in bone size and shape. Here, we examine the Mexican tetra (Astyanax mexicanus), a species of teleost fish comprising of an extant river‐dwelling surface fish and obligate cave‐dwelling fish. These divergent morphs have evolved for thousands of years in drastically different habitats, which have led to diverse phenotypic differences. Among many craniofacial aberrations, cavefish harbor a wider gape, an underbite, and larger jaws compared to surface‐dwelling morphs. Morphotypes are inter‐fertile, allowing quantitative genetic analyses in F₂pedigrees derived from surface × cavefish crosses. Here, we used quantitative trait locus (QTL) analysis to determine the genetic basis of jaw size. Strikingly, we discovered a single genomic region associated with several jaw size metrics. Future work identifying genetic lesions that explain differences in jaw development will provide new insight to the mechanisms driving bone size differences across vertebrate taxa.