Background: Coccidian infection may enhance the proliferation of gut Enterobacteriaceae. Bacterial infections in rabbits can negatively affect the body condition and cause high mortality, especially at young ages. Therefore, the effect of prebiotic supplementation on the presence of Escherichia coli and Salmonella species in rabbits experimentally infected with intestinal coccidiosis was investigated., Methods: Thirty male rabbits aged 35-40 days were divided into three equal groups. These groups were; prebiotic supplemented (PS), positive control (PC), and negative control (NC) groups. The prebiotic group was supplemented with 2 g/L of Bio-Mos ® until the end of the experiment. At day ten post prebiotic supplementation; the PS and PC groups were inoculated orally with 5.0 × 10 4 sporulated oocysts of mixed species of rabbit Eimeria . The daily fecal examination was carried out from the day 4 post-infection (PI) until the day 8 PI. At day 5 and day 8 PI, 5 rabbits from each group (PS, PC, and NC) were humanely slaughtered and parts of intestinal tissue were collected for microbiological analysis., Results: There was a significant decrease ( P ≤ 0.05) in the oocyst count in the PS group (25.12 × 10 4 ± 10.36) when compared with the PC group (43.43 × 10 4 ± 11.52) and this decrease was continued till the end of the experiment. Eleven E. coli isolates were detected in the collected samples with an overall prevalence of 24.4%. The highest prevalence of E. coli was in the PC group (13.33%) while the lowest one was in the PS group (4.44%). Meanwhile, four Salmonella serovars were isolated with an overall prevalence of 8.89%. The NC group showed one serovar (2.22%) and PC revealed three serovars (6.67%) while the prebiotic supplemented group didn't show any salmonella isolate. Of E. coli isolates, five isolates (O78, O125, O152, O115 and O168) showed high resistance to florfenicol and neomycin (100%). Also, of salmonella serovars, thee serovars ( Salmonella entrica subsp. enterica serovar Macclesfield, Salmonella entrica Subsp . enterica serovar Canada and Salmonella entrica Subsp. enterica serovar Kisangani) showed high resistance to sulphamazole, amoxicillin and flumequin (75%) while it was sensitive to levofloxacin and ciprofloxacine (75%). The bacterial colony in this study was the same results at days 5 and 8 PI., Conclusion: The use of prebiotic as prophylaxis in this experiment significantly reduced the prevalence of E. coli and salmonella associated with the intestinal coccidiosis in rabbits., Competing Interests: The authors declare that there are no competing interests., (©2021 Aboelhadid et al.)