To enhance the quality of transmissions, all digital communication systems use error-correcting codes. By introducing some redundancy in the informative binary data stream, they allow one to better withstand channel impairments. The design of new coding schemes leads to a perpetual evolution of the digital communication systems and, thus, cognitive radio receivers have to be designed. Such receivers will be able to blind estimate the transmitter parameters. In this study, an algebraic method dedicated to the blind identification of punctured convolutional encoders is presented. The blind identification of such encoders is of great interest, because convolutional encoders are embedded in most digital transmission systems where the puncturing principle is used to increase the code rate to reduce the loss of the information data rate because of the redundancy introduced by the encoder. After a brief recall of the principle of puncturing codes and the construction of the equivalent punctured code, a new method dedicated to the blind identification of both the mother code and the puncturing pattern is developed when the received bits are erroneous. Finally, case studies are presented to illustrate the performances of our blind identification method.