Axo-glial interactions are required for the organization of highly specialized molecular domains in myelinated axons. The molecular composition of these domains includes cell adhesion molecules, ion channels and cytoskeletal proteins. Recent genetic and molecular studies provide new insights into how these macromolecular complexes are assembled and organized into functional domains, and how the loss of individual components affects domain organization and function. More importantly, the key molecular components identified at the vertebrate axo-glial septate junctions are also present at the Drosophila septate junctions. In addition, new roles for axo-glial paranodal septate junctions have emerged, which suggest that the paranodal region may act as an ionic barrier and a molecular fence in myelinated axons.