We prepared a protamine–monododecyl phosphate composite by mixing protamine (P) and a monododecyl phosphate (MDP). This P–MDP composite formed an acid–base complex by the electrostatic interaction between cationic protamine and the negatively charged phosphate group. Additionally, according to the X-ray diffraction (XRD) measurements, the composite formed a selfassembled lamellar structure with an interaction between the long alkyl chains of MDP. As a result, the P–MDP composite showed the proton conductivity of 9.5 × 10−4 S cm−1 at 120–130 C under anhydrous conditions. Furthermore, the activation energy of the proton conduction of the P–MDP composite was approximately 0.18 eV. These results suggested that the proton conduction of the P– MDP composite was based on an anhydrous proton conductive mechanism. In contrast, the anhydrous proton conduction of the P–methanediphosphonic acid (MP) composite, which did not form the selfassembled lamellar structure, was ca. 3 × 10−5 S cm−1 at 120–130 C and this value was one order of magnitude lower than that of the P–MDP composite. Therefore, the two-dimensional self-assembled proton conductive pathway of the P–MDP composite plays a role in the anhydrous proton conduction.