Evolutionary developmental biology links the key ideas of evolution, such as the study of evolvability, into the study of developmental properties and mechanisms. Biological complexity is recognized as key component of evolvability and the emergence of novel traits. However, the study of complexity and how it factors into evolvability has been mired in inconsistent definitions and the lack of a clear framework including the fact that phenotype is an end result of developmental processes. Complex phenotypes are the result of interactions between intrinsic factors, such as developmental processes and constraints, and extrinsic factors, including selective pressures and environmental stimuli. As such, complexity is tightly regulated and structured through ontogeny. In this thesis, I address the links between complexity, evolvability and the emergence of novelty using the C. eos-neogaeus hybridization complex as a study system. I first explore how the conceptual and methodological frameworks of modularity and integration allow explicit studies of the links between complexity and evolvability. I subsequently contextualize complexity in the framework of epigenetics sensu Waddington and identify hybridization, and hybrid organisms as pertinent models for the study of biological complexity. Using geometric morphometrics, I assess phenotypic integration and modularity in the cranial and postcranial skeleton of the C. eos-neogaeus hybridization complex. I show that hybridization results in varying patterns of modularity and phenotypic integration between parental species and hybrid lineages of the C. eos-neogaeus complex. I show that shared pairwise phenotypic integration between traits result in different effects on the directionality of shape variation across lineages. The modification of the directionality of shape variation, promotes phenotypic transgression and phenotypic novelty in hybrids. Finally, I explored topological variation and integration in the pectoral girdle across hybrid lineages and parental species of the C eos-neogaeus complex. I identify conserved patterns of modularity in the pectoral girdle within the C. eos-neogaeus complex despite lineage-specific variation in structure and the shape of individual bones within the pectoral girdle. While the factors promoting increases and decreases in complexity through evolution require further attention, my thesis illustrates how modularity and integration are crucial in organizing and maintaining complexity within and between species.