The sizes of body parts often co-vary through exponential scaling, known as allometry. The evolution of allometry is central to the generation of morphological diversity. To make inferences regarding the evolved responses in allometry to natural and artificial selection, we compared allometric parameters (slope and intercept) among seven species and breeds of domestic bovids using cross-sectional ontogenetic data and attempted to interpret the differences in these parameters. The allometric slopes were not different among some species, whereas those between breeds within species were, indicating that the slopes were typically invariant but could be changed under strong, specific selection. With the exception of yak, the differences in the intercept independent of the slopes (the alternative intercept) among species might better correspond to their divergence times than the differences in allometric slope, and the remarkably higher alternative intercept found in yaks can be explained by their unique morphological evolution. These findings provide evidence that differences in the alternative intercept can retain traces of the phylogenetic changes derived from differentiation and evolution.