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The microbiological quality of chicken meat in the Southeast District of Botswana’s retail market was assessed. The study focused on peri-urban and urban areas surrounding Gaborone: Phakalane, Ledumang, Gaborone Bus Rank (GBS), Ramotswa, and Tlokweng. A total of 30 chicken carcasses (six samples for each site) in their original packaging material were collected from randomly selected retail shop within each site. The result showed that GBS sample had the highest Total Viable Count (7.03 log₁₀ CFU/g), followed by Ledumang (6.89 log₁₀ CFU/g) and Ramotswa (6.52 log₁₀ CFU/g), respectively. These findings suggest possible poor hygiene in retail establishments. The lowest TVC was observed for Phakalane (5.93 ± 0.18 log₁₀ CFU/g). Presumptive coliform counts in most sampling sites exceeded 6 log₁₀ CFU/g in Violet Red Bile Agar (VRBA) media, suggesting poor handling practices of possible faecal contamination of chicken meat. Additional microbial counts from Campylobacter Chloraphenicol agar, Hektoen Enteric agar, and Baird-Parker agar further highlights potential presence of spoilage organisms in the meat. With 16 S rRNA gene sequencing molecular identification and biochemical tests Campylobacter, Staphylococcus aureus and Salmonella were not detected. Nevertheless, Escherichia coli, Aeromonas spp., Proteus mirabilis, Mammaliicoccus spp. and Serratia spp. were identified as predominant genera across the district respectively. Other identified opportunistic microorganisms include Pseudomonas aeruginosa, Macrococcoides caseolyticum and Hafnia alvei. Although not key pathogens, detection of Comamonas and Lelliottia genera indicates poor hygiene. The Phylogenetic tree analysis confirmed the taxonomic relatedness of isolates, suggesting possible cross-contamination from shared sources. In overall these findings underscore the need for stricter food hygiene measures and frequent microbiological monitoring to ensure food safety in the study area.