Capparis spinosa and C. decidua are indigenous medicinal plants of Pakistan which are rich in antioxidant compounds. In present investigation, the aqueous menthanolic, ethanolic and acetone extracts of stem bark, shoot, fruit, flower and roots of both species were investigated for their antimicrobial potential in comparison with amoxicillin and ciprofloxacin (control). The effect of these extracts was evaluated on the growth of four bacteria i.e., Staphylococcus aureus, Escherichia coli, Bacillus subtilis and Pasteurella multocida using disc diffusion and minimum inhibitory concentration (MIC) assays. After comparing all extracts, it was found that methanolic extracts of selected parts of both species significantly reduced the growth of all four bacteria although different extracts expressed varying efficacy in reducing bacterial growth. It was further noted that S. aureus growth was mainly inhibited by methanolic extracts of C. decidua flowers and roots (GIZ: 26.5 and 26.4 mm, respectively), E. coli population was effectively reduced by methanolic extracts of C. decidua roots and shoots (GIZ: 29.1 26.7 mm, respectively) while B. subtilis growth was inhibited maximally by methanolic extracts of C. spinosa stem bark and C. decidua fruits (GIZ: 26.8 and 26.8, respectively). Moreover, methanolic extract of C. decidua root markedly inhibited the growth of P. multocida (25.7 mm). On the basis of above mentioned findings, it can safely be concluded that C. decidua possess higher antimicrobial potential than C. spinosa and these can be used as natural antibacterial agent.