Carboxyl terminal processing protease of D1 protein (CtpA) catalyzes carboxyl terminal processing of D1 protein, which is predicted to be an excellent target for a general broad-spectrum herbicide. In this study, the CtpA gene from spinach cDNA was cloned and overexpressed and the recombinant CtpA fusion protein (rCtpA) was used as antigen to immunize BALB/c mice for the production of monoclonal antibody (MAb). Western blot and ELISA results indicated that both rCtpA and the PDZ domain protein of CtpA had specific binding abilities to MAbs, while the specificity and sensitivity of rCtpA were much higher than that of the PDZ domain. These results suggest that parts of the antigen determinant of CtpA were located in the PDZ domain. The MAbs and related results obtained in this study proved the feasibility of high-throughput screening of lead compounds for protease as inhibitors and mechanism analysis of CtpA enzyme.