Polydopamine is the first adhesive polymer that can functionalize surfaces made of virtually all material chemistries. The material-independent surface modification properties of polydopamine allow the functionalization of various types of medical and energy devices. However, the mechanism of dopamine polymerization has not yet been clearly demonstrated. Covalent oxidative polymerization via 5,6-dihydroxyindole (DHI), which is similar to the mechanism for synthetic melanin synthesis, has been the clue. Here, it is reported that a physical, self-assembled trimer of (dopamine)2/DHI exists in polydopamine, which has been known to be formed only by covalent polymerization. It is also found that the trimeric complex is tightly entrapped within polydopamine and barely escapes from the polydopamine complex. The result explains the previously reported in vitro and in vivo biocompatibility. The study reveals a different perspective of polydopamine formation, where it forms in part by the self-assembly of dopamine and DHI, providing a new clue toward understanding the structures of catecholamines such as melanin.