A membrane electrode assembly includes a proton exchange membrane, an anode and a cathode. The proton exchange membrane has two opposite surfaces, a first surface and a second surface. The anode is located adjacent to the first surface of the proton exchange membrane, and the cathode is located adjacent to the second surface of the proton exchange membrane. The anode includes a diffusion layer and a catalyst layers. The diffusion layer includes a carbon nanotube structure. A biofuel cell using the membrane electrode assembly is also provided.