The emergence of multidrug-resistance (MDR) bacteria poses a health threat to the public. This is seen among the extended spectrum β-lactamase (ESBL) producing Enterobacteriaceae family often mediated by blaTEM and blaCTX-M genes. This study evaluates the molecular characteristics of ESBL-producing P. mirabilis isolated from Klang River, Malaysia. The physiochemical properties of the Klang River were determined. 150 water samples were collected, which 546 Gram-negative bacilli were detected. 39 (26.0%) P. mirabilis were isolated and tested against β-lactam antibiotics. 21 (53.8%) exhibited MDR, which 15 (71.4%) were ESBL-producing strains after screening with PCR and genetic sequencing approaches. Among the 15, 3 strains (20%) exhibited blaTEM gene and 12 (80%) exhibited blaCTX-M gene. Molecular docking was performed to understand the structure of the mutated β-lactamase. Findings suggest high prevalence of blaTEM and blaCTX-M genes among P. mirabilis strain isolated. There is a need of advanced molecular techniques to further elucidate MDR bacteria.