Pseudomonas sp. M18 is one of plant growth-promoting rhizobacteria capable of producing two kinds of anti-fungal agents: phenazine-1-carboxilic acid (PCA) and pyoluteorin (Plt). The pqsR gene, which encodes a LysR family member PqsR, was amplified from chromosomal genome of strain M18. Using the homologous recombination technique, a chromosomal pqsR inactivated mutant strain M18PRG was constructed in Pseudomonas sp. M18. To study the effect of pqsR gene on Plt biosynthesis, the dynamic curves of Plt production by strains M18 and M18PRG was measured in KMB media. As a result, Plt production of the pqsR mutant was three to four folds higher than that of its parent strain M18. The Plt production was restored to the wild-type level when strain M18PRG was complemented with pqsR gene in trans. The regulation of pqsR gene on Plt production was further confirmed by the pltA′-′lacZ translational fusion analysis. These results indicate that pqsR gene negatively controls the Plt biosynthesis. Additionally, by analyzing the growth curves of wild type strain M18 and pqsR mutant, we can readily find that PqsR has a negative influence on cell growth. It was also shown that the production of red pigments in strain M18 required the expression of pqsR gene. In conclusion, the data presented in this study clearly demonstrate that PqsR acts as a global regulator involved in many physiological activities in Pseudomonas sp. M18.