Drought stress is one of the major yield affecting factor for pepper plant. The effects of PGPRs were analyzed in relation with drought resistance. The PGPRs inoculated pepper plants tolerate the drought stress and survived as compared to non-inoculated pepper plants that died after 15 days of drought stress. Variations in protein and RNA accumulation patterns of inoculated and noninoculated pepper plants subjected to drought conditions for 10 days were confirmed by two dimensional polyacrylamide gel electrophoresis (2D-PAGE) and differential display PCR (DD-PCR), respectively. A total of six differentially expressed stress proteins were identified in the treated pepper plants by 2D-PAGE. Among the stress proteins, specific genes of Cadhn, VA, sHSP and CaPR-10 showed more than a 1.5-fold expressed in amount in B. licheniformis K11-treated drought pepper compared to untreated drought pepper. The changes in proteins and gene expression patterns were attributed to the B. licheniformis K11. Accordingly, auxin and ACC deaminase producing PGPR B. licheniformis K11 could reduce drought stress in drought affected regions without the need for overusing agrochemicals and chemical fertilizer. These results will contribute to the development of a microbial agent for organic farming by PGPR.