Hybridization can generate phenotypes departing from the parental range through many processes: increased variance due to increased heterozygosity, decreased phenotypic integration and altered covariation structure due to changes in the expression of (co)variation generating developmental processes, and transgression that may arise from epistasis and compensatory genes. Morphometric assessment of shape differentiation, variance and covariance may shed light on these processes, especially for complex characters for which the genetic basis has not yet been assessed. The shape of the first upper molar was thus quantified in a cross between inbred strains of the two European subspecies of the house mouse (Mus musculus domesticus and M. m. musculus). Hybrids appeared as moderately transgressive. Morphological variance was increased in F2s, back to levels observed in wild populations. The pattern of variance–covariance was different between the two parental strains, but restored to a wild-type structure in F2s. Finally, F2s displayed a degree of morphological integration comparable to wild populations but lower than observed in the parental strains. This is interpreted as the result of the reshuffling of the standing genetic variation in hybrids that should have restored the expression of (co)variance generating processes made ineffective in parents due to random allele fixation of some loci. Inter-parental differentiation was more important in regions of the tooth developing early during embryogenesis, whereas transgression was more pronounced in late developing regions. Mutations may more easily generate important geometric differences early during tooth development, occurring as a cascade of signalization from the first cusp to initiate onward. Epistasis and constraints of neighboring parts may be more important later, promoting transgression and impeding differentiation.