Background: Contamination of natural niches with pharmaceutical residues has emerged out as a serious concern. Disposal of untreated effluents from the pharmaceutical, hospital, and domestic settings has been identified as a significant source of such a massive spread of antibiotics. The unnecessary persistence of pharmaceutical residues including antibiotics has been related to the increased risk of resistance selection among pathogenic and non-pathogenic microorganisms. To date, several methods have been devised to eliminate such pollutants from wastewater, but their implication on larger scales is not feasible due to complexities and high costs of the processes, especially in developing and underdeveloped countries. This study aimed to isolate and characterize bacterial strains from domestic and pharmaceutical effluents having biotransformation potential towards most persistent antibiotics. Results: Antibiotic resistance screening and MIC determination experiments indicated highest resistivity of three bacterial isolates against two antibiotics Erythromycin and Sulfamethoxazole-trimethoprim, evincing extensive usage of these antibiotics in our healthcare settings. These isolates were identified as Comamonas jiangduensis, Aeromonas caviae and Aeromonas hydrophila by 16S rDNA sequencing. Growth conditions including incubation temperature, initial pH and inoculum size were optimized for these strains. Successful biotransformation of Erythromycin and Sulfamethoxazole-trimethoprim was achieved within 92 h under optimum growth conditions. Conclusions: Aeromonas and Comononas species were found to be potent degraders of antibiotics tested, presenting these strains as potential candidates to be utilized in the remediation processes.