Polydopamine is not only a multifunctional biopolymer with promising optoelectronic properties but it is also a versatile coating platform for different surfaces. The structure and formation of polydopamine is an active area of research. Some studies have supposed that polydopamine is composed of covalently bonded dihydroxyindole, indoledione, and dopamine units, but others proposed that noncovalent self-assembly contributes to polydopamine formation as well. However, it is difficult to directly find the details of supramolecular structure of polydopamine via self-assembly. In this study, we first report the graphite-like nanostructure observed in the carbonized polydopamine nanoparticles in nitrogen (or argon) environment at 800 degrees C. Raman characterization, which presents the typical D band and G band, confirmed the existence of graphite-like nanostructures. Our observation provides clear evidence for a layered-stacking supramolecular structure of polydopamine. Particularly, the size of graphite-like domains is similar to that of disk-shaped aggregates hypothesized in previous study about the polymerization of 5,6-dihydroxyindole [Biomacromolecules 2012, 13, 2379]. Analysis of the hierarchical structure of polydopamine helps us understand its formation.