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Aims: The aim of this study is to investigate the antimicrobial activities of aqueous and ethanolic (EtOH) extracts of orange (C. sinensis Pers.) and lime (C.aurantifolia (Christm.) Swingle) peels on some selected pathogenic bacteria isolated from jollof rice. Study Design: Antimicrobial analysis, phytochemical analysis Place and Duration of Study: Microbiology Laboratory, Department of Biological Sciences, Wesley University Ondo, Ondo State, Nigeria, between June and July 2017. Methodology: Antimicrobial analysis of aqueous and EtOH extracts prepared from orange and lime peels were done by using the agar well diffusion method against the selected pathogenic bacteria. The extracts were screened for anti-nutrients such as alkaloids, tannins, oxalate, phytate and glycosides. Results: The EtOH extracts of orange peel showed a remarkable zone of inhibition against Escherichia coli (23.5 ± 0.1 mm) followed by Staphylococcus aureus (11.4 ± 0.0 mm) and Bacillus cereus (9.8 ± 0.0 mm). Whereas, the aqueous extracts of orange showed no zone of inhibition against the tested pathogenic bacteria. In addition the EtOH peel extract of lime showed maximum zone of inhibition against  S. aureus (15.5 ± 0.0 mm) followed by E. coli (14.3 ± 0.1 mm) and B. cereus (12.1 ± 0.2 mm), whereas its aqueous peel extract showed no zone of inhibition against K. pneumonia, S. aureus, E. coli and B. cereus. Both EtOH extracts of orange and lime peels showed no zone of inhibition against K. pneumonia. Streptomycin, the reference antibiotic, had no zone of inhibition against B. cereus and S. aureus whereas it recorded maximum zone of inhibition against E. coli (24.0 ± 0.0 mm) and K. pneumonia (25.1 ± 0.1 mm). The phytochemical analysis showed presence of oxalate, alkaloids, phytate, tannins and glycoside in the aqueous and EtOH extracts of lime and orange peels. The antimicrobial activities of EtOH extracts of both lime and orange peels demonstrated inhibitory effect against the targeted organisms such as B. cereus, S. aureus and E. coli. Conclusion: The exploration of novel antimicrobial agents from natural resources such as plant like Lime and sweet orange as food preservative is due to the presence of various secondary metabolites.