Pseudomonas aeruginosa is a major cause of nosocomial infections due to its high drug resistance. From 180 clinical specimens, 50 isolates were obtained from ear swabs, burn wounds, sputum, urine, and wound samples. This study investigated quorum sensing genes (pqsA, pqsB, pqsC, pqsD) and their association with multidrug resistance (MDR). Nineteen isolates (38%) were multi-drug resistant (MDR) and 31 (62%) were non‑MDR. PCR analysis demonstrated detection rates of 89.5% for pqsA, 94.7% for pqsB, 94.7% for pqsC, and 73.7% for pqsD. Antibiotic susceptibility testing revealed the highest resistance to colistin (84%) and imipenem (76%), with moderate resistance to ciprofloxacin (32%) and tobramycin (30%). Lower resistance was observed for meropenem (16%), piperacillin/tazobactam (12%), gentamicin (10%), amikacin (8%), and ticarcillin/clavulanic acid (4%). The presence of Pseudomonas Quinolone Signal (PQS) genes was significantly associated with increased resistance to all tested antibiotics (p ≤ 0.01). These findings highlight the contribution of the PQS system to virulence and biofilm formation, indirectly supporting antibiotic tolerance and persistence in MDR P. aeruginosa. This is study provides the first molecular evidence from Iraq linking pqsABCD quorum sensing genes with resistance to antibiotics in clinical Pseudomonas aeruginosa isolates, offering new insight into the contribution of the PQS system to antibiotic tolerance and persistence.