Biological variation in the mammalian skull is the product of a series of factors including changes in gene expression, developmental timing, and environmental pressures. When considering the diversity of extant mammalian crania, it is important to understand these mechanisms that contribute to cranial growth and in turn, how differences in cranial morphology have been attained. Various researchers, including Dr. Sue Herring, have proposed a variety of mechanisms to explain the process of cranial growth. This work has set the foundation on which modern analysis of craniofacial morphology happens today. This study focused on the analysis of modularity in three mammalian taxa, all of which exhibit facial reduction. Specifically, we examined facial reduction as a morphological phenomenon through the use of two-module and six-module modularity hypotheses. We recorded three-dimensional coordinate data for 55 cranial landmarks that allowed us to analyze differences in cranial shape in these three taxa (primates n = 88, bats n = 64, dogs n = 81). When assessing modularity within the two-module modularity hypothesis specifically, dogs exhibited the lowest levels of modularity, while bats and primates both showed a slightly more modular covariance structure. We further assessed modularity in the same sample using the Goswami six-module model, where again dogs exhibited a low degree of modularity, with bats and primates being more moderate. We then broke the sample into subsets by analyzing each morphotype separately. We hypothesized that the modularity would be more pronounced in the brachycephalic morphotype. Surprisingly, we found that in brachycephalic dogs, normocephalic dogs, brachycephalic primates, and normocephalic primates, there was a moderate degree of modularity. Brachycephalic bats had a low degree of modularity, while normocephalic bats were the most modular group observed in this study. Based on these results, it is evident that facial reduction is a complex and multifaceted phenomenon with unique morphological changes observed in each of the three taxa studied.