A geometric morphometric analysis of the form of the marmot ventral cranium and mandible was carried out. Allometry was found to play an important role in shaping both these structures, and, although allometric trajectories were species-specific, similar shape changes were observed during ventral cranial and mandibular growth. Most of the ontogenetic shape changes occur in regions involved in the mechanics of mastication and bite. Sexual dimorphism is manifest mainly size. The interspecific comparison of ventral crania from all living marmot species produces results only partially congruent with those obtained for the mandible or with the marmot molecular phylogeny. The phylogenetic signal in the ventral cranium seems weaker than in the mandible, and the morphological clusters do not reflect evident size or ecological similarities. The ventral cranium could have limited evolutionary plasticity due to its complexity, and, thus, it may have retained plesiomorphic characters which contribute to mask the phylogenetic signal.