The present research was conducted for molecular characterization of important zoonotic bacteria isolated from different samples in ostrich and also determined their antimicrobial activity. For this current research, 32 samples were randomly collected from 8 ostriches at different ages, of which 8 were oropharyngeal, 8 were cloacal swabs, 8 were environmental sand samples, and 8 were feces samples. In addition, the bacteria were isolated and identified by using standard microbiological methods, including cultural, biochemical and molecular techniques. 16S rRNA gene was used to detect Escherichia coli and Salmonella spp. molecularly. The Kirby-Bauer disc diffusion method was used to determine the antibiotic sensitivity test. Out of 32 samples, E. coli 8 (53.33%) and Salmonella spp. 7 (46.67%) were identified in young ostrich, while in adult ostrich, E. coli 2 (40%) and Salmonella spp. 3 (60%) were detected. According to our study, E. coli was the most predominant isolate found in cloacal swabs and ostrich feces. Escherichia coli were most sensitive to Amoxicillin and Azithromycin (100%), followed by Kanamycin, Chloramphenicol and Gentamicin (75%), while 100% resistant to Piperacillin, Bacitracin, Tetracycline, Cloxacillin, Novobiocin, Cefixime. Salmonella spp. was 100% sensitive to Azithromycin and also 100% resistant to Tetracycline, Piperacillin, Bacitracin, Chloramphenicol and Methicillin. Our research concluded that E. coli and Salmonella spp. are multi-drug resistant bacteria, and appropriate antibiotics should be used in ostrich farms to protect the multi-drug resistant bacteria. We suggest farm owners increase public awareness about zoonotic diseases and those working on ostrich farms.