Abstract Background Pseudomonas aeruginosa is among the most important cause of life threatening hospital acquired infections. It is considered as top listed public health threat worldwide due to its ability to produce toxins, virulence factors, biofilms and resist multiple antibiotics. Biofilm formation is a pathogenic mechanism harboured by this pathogen which further elevates its resistance to antibiotics and host defence system. Objectives To detect the phenotypic and genotypic biofilm forming potential and its association with multi drug resistance in P. aeruginosa clinical isolates. Methods In the present study, isolation of P. aeruginosa was performed by conventional and molecular method using polymerase chain reaction (PCR) from (n=200) clinical samples. Kirby Bauer method was performed for detection of MDR isolates. The biofilm forming ability of P. aeruginosa isolates was detected by microtitre plate assay (MPA) while the genes associated with biofilm formation (pelA and pslA) were detected by PCR. Results The results of study revealed that P. aeruginosa was detected in 26% (52/200) isolates with highest frequency 38.63% in burn wound samples followed by 22.22% in sputum samples and 20.58% in surgical wound samples. Highest resistant was found to ceftriaxone (94%) followed by meropenem (92%), imipenem (90%) and cefotaxime (90%) while (n=20) isolates were detected as MDR. Biofilm formation of variable degree was detected in 49 (94%) isolates. Additionally it was recorded that all the MDR isolates exhibits biofilm formation including 55% as moderately, 40% as strongly and 5% as weakly adherent. Among the MDR P. aeruginosa, the biofilm-associated gene pelA was detected in 95% while pslA was found in 90% isolates. Conclusions It was concluded that biofilm forming P. aeruginosa are more resistant to tested antibiotics and strongly linked with presence of pelA and pslA genes. This presence of MDR strains along with biofilm formation is depicting a lethal combination of bacterial armory that poses a serious threat for public health.