The plant growth promoting rhizobacteria (PGPR) strains Bacillus subtilis AH18 and Bacillus licheniformis K11 were selected as biocontrol agents for the suppression of phytophthora blight caused by Phytophthora capsici. A genetic monitoring method was developed utilizing multiplex and real-time polymerase chain reaction (PCR) in a pepper farming soil. 2,3-Dihydro-2,3-dihydroxy benzoate dehydrogenase of a key siderophore synthesis enzyme (sid), auxin efflux carrier gene (aec), and cellulase gene (cel) of B. subtilis AH18 were used as genetic methods to monitor the presence and concentration of the inoculated microbial agents. Monitoring of B. licheniformis K11 was carried out by amplification of a cellulase gene (celK), siderophore synthase gene (dhbF), and iturin synthase A gene (ituA). B. subtilis AH18 and B. lichenifomis K11 could be detected upto 20 days by multiplex PCR in pepper farming soil. B. subtilis AH18 sid and three Bacillus lichenifomis K11 genes could be detected upto week 5 by real-time PCR in the natural unsterilized soil. P. capsici pathogen became nearly undetectable after 20 days biocontrol treatment in the field soil. These results could lead to the development of select PGRPs as useful microbial agents for the organic farming of peppers.