Abstract The aim of this study was to find biocatalyst which uses thebaine and extract of different parts of Papaver bracteatum to synthesize morphine alkaloids. The thebaine-resistant strains were obtained from microbial flora of different parts of P.bracteatum. They were purified and treated utilizing different concentrations of thebaine. Those that can grow at a concentration of over 500 µg/ml were chosen for the biotransformation experiments. Biotransformation experiments were carried out utilizing selected cells in the medium containing thebaine and/or the extract of P.bracteatum; the products of such biotransformation were extracted and the profiles of metabolites were evaluated using HPTLC, and LC/ESI-MS methods. Thereafter, the effective isolate for thebaine transformation was characterized by physiological, biochemical and biomolecular methods. The results show that among 67 isolates, 12 strains were selected using the HPTLC screening as candidates that can transform thebaine into codeine and morphine. Among them, 5 strains were identified to transform plant extract, among which, using LC/ESI-MS, a candidate was selected and identified as Bacillus sp. FAR. It can be concluded from this study, that this microbial flora candidate can transform thebaine into important narcotic drugs and it will be a valuable step in biotechnology.