Pseudomonas aeruginosa (Pa) is a versatile opportunistic pathogen. Quorum sensing (QS) is essential for Pa pathogenicity by activating virulence factor production. Among the three known QS systems in Pa, Pseudomonas Quinolone Signal (PQS) is an alkyquinolone, one of >50 quinolone compounds produced that differ in alkyl chain length and desaturation. The condensing enzyme PqsD catalyzes the branching point of quinolone synthesis, utilizing either malonyl‐CoA or 3‐oxo‐fatty acids of various chain lengths. We showed that PqsD exhibited higher activity using fatty acid substrates with 10, 12 or 14 carbons than those with 6 or 8 carbons, suggesting the fatty acid chain length is critical in positioning the carboxylic group for efficient catalysis. In addition, PqsD showed preference for malonyl‐CoA over 3‐oxo‐decanoic acid in vitro. Alanine mutants of the active site triad (C112, H257, and N287) were assayed for PqsD activity. All 3 residues were essential for condensation, whereas N287 was not required in the formation of anthraniloyl‐PqsD intermediate. Inhibitors of PqsD were identified by virtual screen and the IC50s of the top‐scoring hit compounds were determined. Our results suggest that regulation of the substrate supply in vivo may be important in determining the composition of quinolone compounds, which in turn affect the virulence factor production in Pa. (Supported by NIH P20 RR017677 and UL1 RR029882)