The production of monoclonal antibodies (MAb) specific to microbes is rapidly growing. Finding an appropriate antigen to screen hybridoma clones has become increasingly important. However, the conventional method, in which the purified antigen from the microbe is routinely used for screening, cannot avoid selection of false positive hybridoma clones, since even highly purified antigen is found to be contaminated with some other proteins from the microbe. In this study, MAbs against anthrax protective antigen (PA), the central component of the three-part toxin secreted by Bacillus anthracis were developed using a pair of the roughly purified native PA as an immunogen and the recombinant PA as a screening antigen without any possibility of false selection, since the recombinant PA was produced by a gene engineering approach and impossible to be contaminated with any other proteins from B. anthracis. In total, nine stable hybridoma clones secreting anti-PA MAbs were developed. All of them had the same type of heavy and light chains, IgG1/kappa. The binding profiles for these anti-PA MAbs were investigated by ELISA. This novel approach to the development of MAbs should be applicable to the production of MAbs to other microbes, especially to those from which antigens can hardly be purified to a high degree.