Considering the side effects of pesticides on ecosystems, use of safe antimicrobial compound is very important. In this study, the antibacterial effect of aqueous extracts of Achillea santolina and bark of pomegranate fruit was investigated against four bacterial strains namely, Bacillus sp., Pseudomonas sp., Agrobacterium tumefaciens and Xanthomonas citri. The plant extracts were prepared by maceration method. In vitro antibacterial activity of extracts was evaluated by the well diffusion method. The concentrations of extracts were adjusted at 25, 50,100 and 200 mg/ml. Distilled water and gentamycin disk (10μg/disk) were used as negative and positive controls respectively. The experiment was performed as completely randomized design with four replications. The diameters of inhibition growth zones were measured. The data were analyzed by SAS software. According the results, the antibacterial activity of extracts was significantly different. The sensitivity of bacteria to extracts was also different. Generally, the antibacterial activity of Achillea santolina extract was more than pomegranate fruit bark extract. At 25 and 50 mg/ml concentrations, none of extracts showed antibacterial effect on investigated bacteria. The most antibacterial effect was at 200mg/ml concentration on Bacillus sp. for both extract. The mean of inhibition zone of this concentration (1.4 and 1.36 cm for pomegranate fruit bark and Achillea santolina respectively) had no significant difference with inhibition zone of gentamycin disk (1.4cm). The Achillea santolina extract at 200mg/ml had also significant antibacterial effect on Pseudomonas sp. and its inhibition zone had no significant difference with gentamycin disk. The extract of pomegranate fruit bark at concentrations achieved in this study, didn’t show any antibacterial effect on Pseudomonas tolaasii . The growth inhibition zones of A. tumefaciens at 100 and 200 mg/ml concentrations of both extracts were not significantly different and also were significantly less than inhibition zone of gentamycin. Noticeably, both extracts had no antibacterial effect on Xanthomonas citri at none of investigated concentrations, so that the diameter of growth inhibition zones was zero. Minimum inhibitory concentration (MIC) of pomegranate fruit bark extract was determined as 25 mg/ml and 12.5 mg/ml for Pseudomonas tolaasii and Bacillus sp. respectively and MIC of Achillea santolina extract for Bacillus sp. was determined as 12.5 mg/ml. The results of this study indicated that aqueous extract of Achillea santolina has considerable antibacterial effect on Pseudomonas tolaasii and Bacillus sp.