The invention and the diffusion of environmental process of production and consumption goods are impeded by two market failures: the first on environment and the second on knowledge. The question arises whether the instruments aiming at correcting these market failures should be jointly designed or not. We investigate this question for a major instrument of support to innovation: the patent system. We demonstrate that a patent system and a discriminating environmental taxation that are jointly defined provide for a greater efficiency. We conclude that the two externalities interact with each other through the patent system.