Ion channels mediate selective passive transport of ions across biomembranes. They participate in diverse physiological processes and belong to distinct protein families. Understanding specific roles of different channels in physiology, pathology, and pharmacology requires knowledge of their origin and evolution. Traditional approaches include experimental physiological studies and analysis of sequences and genomes. In the last two decades, availability of 3D structures of many ion channel proteins revolutionized ion channel studies, including their evolution. In this chapter, we consider examples of how 3D structures provided clues for understanding evolutionary aspects of multi-domain organization, domain folding, and roles of highly conserved and variable residues. Such achievements are important for addressing practical problems including drug design, channelopathies, and acquired resistance to insecticides.