Atomic defects in crystalline structures have pronounced affects on their bulk properties. Aberration-corrected transmission electron microscopy has proved to be a powerful characterization tool for understanding the bonding structure of defects in materials. In this article, recent results on the characterization of defect structures in two dimensional materials are discussed. The dynamic behavior of defects in graphene shows the stability of zigzag edges of the material and gives insights into the dislocation motion. Polycrystalline graphene is characterized using advanced electron microscopy techniques, revealing the global crystal structure of the material, as well as atomic-resolution observation of the carbon atom positions between neighboring crystal grains. Studies of hexagonal boron nitride (hBN) are also visited, highlighting the interlayer bonding, which occurs upon defect formation, and characterization of grain boundary structures. Lastly, defect structures in monolayer polycrystalline transition metal dichalcogenides grown by CVD are discussed.