The notion of modularity has become a unifying principle to understand structural and functional aspects of biological organization at different levels of complexity. Recently, deciphering the modular organization of molecular systems has been greatly aided by network theory. Nevertheless, network theory is completely absent from the investigation of modularity of complex macroscopic phenotypes, a fundamental level of organization at which organisms experience and interact with the environment. Here, we used geometric descriptors of phenotypic variation to derive a network representation of a complex morphological structure, the mammalian mandible, in terms of nodes and links. Then, by integrating the network representation and description with random matrix theory, we uncovered a modular organization for the mammalian mandible, which deviates significantly from an equivalent random network. The modules revealed by the network analysis correspond to the four morphogenetic units recognized for the mammalian mandible on a developmental basis. Furthermore, these modules are known to be affected only by particular genes and are also functionally differentiated. 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