Myelinated axons are segregated into molecular domains that are essential for action potential propagation. Each domain is characterized by clustering of specific molecular components and disruption of these domains, as seen in multiple sclerosis and ataxias, results in altered neuronal function. However, mechanisms responsible for domain organization remain elusive. We utilized mouse conditional knockouts to uncover mechanisms responsible for the organization and maintenance of the paranode, juxtaparanode, and axon initial segment (AIS). Paranode disruption results in mislocalization of juxtaparanodal proteins and disorganization of the axonal cytoskeleton. Caspr and Caspr2, which localize to the paranode and juxtaparanode, contain binding sites for the cytoskeletal adaptor protein 4.1B. We generated 4.1B null mice and showed that loss of 4.1B resulted in severe disorganization of the juxtaparanode in both the peripheral (PNS) and central nervous system (CNS). At P30 PNS paranodes, loss of 4.1B disrupted Caspr localization and AGSJs. Loss of 4.1B at CNS paranodes resulted in progressive disruption of Caspr and AGSJs. Thus, 4.1B plays a role in interactions between the paranodal AGSJs and axonal cytoskeleton and is required for long-term maintenance of axonal domains. The cerebellar Purkinje AIS is targeted by basket axon collaterals that form the pinceau, which is critical for cerebellar function. Mechanistic details of pinceau organization are poorly understood. Loss of cytoskeletal adaptor protein AnkyrinG results in mislocalization of the cell adhesion molecule Neurofascin (Nfasc) at the Purkinje AIS and abnormal organization of the pinceau. We generated cell type-specific Nfasc null mice and found that Purkinje Nfasc is required for AIS maturation and for maintaining stable contacts between basket axon terminals and the Purkinje AIS during pinceau organization, while basket neuron Nfasc is required for proper basket axon collateral outgrowth and targeting to Purkinje soma/AIS. Disruption of the AIS and pinceau from loss of Nfasc leads to Purkinje neuron degeneration and ataxia. Together, the results presented in this dissertation elucidate mechanisms responsible for organization of the paranode, juxtaparanode, AIS, and pinceau. This knowledge will be critical for designing future therapeutic strategies to treat pathologies where restoration of axonal domains will be required to restore neuronal function.