Bacillus subtilis antibiotic resistant strains used in oral bacteriotherapy were tested for the resistance to new therapeutically useful antibiotics. Chromosomal mutations originally selected in these strains proved to confer resistances also to these antibiotics. To investigate the stability of the antibiotic resistance markers present in B. subtilis O/C, T, N/R, SIN strains, we considered resistances to Chloramphenicol, Tetracycline, Rifampicin and Streptomycin. Resistances to Tetracycline, Rifampicin and Streptomycin were stably maintained for at least 200 generations in the absence of selective pressure. Chloramphenicol resistance proved to be inducible, showing a progressive loss when the resistant strain was grown in the absence of the antibiotic and a return to its original resistance levels after growth in the presence of the antibiotic. By in vitro and in vivo experiments we demonstrated the absence of homologous transfer of resistance markers among the resistant strains.