ABSTRACT: The vast spread of multidrug-resistant bacteria has encouraged researchers to explore new antimicrobial compounds. This study aimed to investigate the phytochemistry and antibacterial activity of Cycas thouarsii R.Br. leaves extract against Klebsiella pneumoniae clinical isolates. The minimum inhibitory concentration (MIC) values of C. thouarsii extract ranged from 4 to 32 µg/mL. The impact of the treatment of the isolates with sub-inhibitory concentrations of C. thouarsii extract was investigated on the bacterial growth, membrane integrity, inner and outer membrane permeability, membrane depolarization, and bacterial morphology using a scanning electron microscope (SEM) and on the efflux activity using qRT-PCR. Interestingly, most K. pneumoniae isolates treated with C. thouarsii extract showed growth inhibition-a decrease in membrane integrity. In addition, we observed various morphological changes, a significant increase in inner and outer membrane permeability, a non-significant change in membrane depolarization, and a decrease in efflux activity after treatment. The phytochemical investigation of C. thouarsii extract revealed the isolation of one new biflavonoid, 5,7,7″,4‴-tetra-O-methyl-hinokiflavone (3), and five known compounds, stigmasterol (1), naringenin (2), 2,3-dihydrobilobetin (4), 4',4‴-O-dimethyl amentoflavone (5), and hinokiflavone (6), for the first time. Moreover, the pure compounds' MICs' ranged from 0.25 to 2 µg/mL. Thus, C. thouarsii could be a potential source for new antimicrobials.