The study was conducted from November 2012 to June 2013 to isolate aerobic bacteria residing in the eye of working donkeys. Forty five apparently healthy donkeys (APHDE) and 45 donkeys with clininicaly diagnosed ocular disease (DCDO) were used for the study. Swabs were collected from the conjunctiva. Isolation and identification of the bacteria was under aerobic condition. Each of the samples collected yielded at least one bacterium species .A total of 256 bacteria species were recovered from both groups of donkeys. The majority 189/256 (73.8%) of the isolates were Gram- positive and the rest 67/256 (26.2%) were Gram- negative. Bacterial isolates identified in order of magnitude were coagulase negative staphylococcus species (27%), Pseudomonas species (22%), Corynbacterium species (19.9%), Staphylococcus aureus (15%), Streptococcus species (7 %), Escherichia coli (5%), and Bacilli species (4%). There was no statistically significant difference (p>0.05) in the isolation rate of Staphylococcus aureus, Streptococcus species, Pseudomonas species and Bacillus species between APHDE and DCDO. The isolation rate of Coagulase negative staphylococcus species was higher in apparently healthy donkeys and this was statistically significant (p<0.05). Corynbacterium species and Escherichia coli were isolated at higher rate in donkeys with clininicaly diagnosed ocular disease and this was statistically significant (p<0.05). The result indicated the predominance of Gram- positives in both cases (p<0.05). Bacteria were recovered at a higher rate (1.47) in APHDE than the rate in DCDO (1.38).The quality of bacteria isolated in both cases was comparable except Escherichia coli which were not recovered from APHDE. Isolation of most bacteria both from APHDE and DCDO might suggest that the bacterium which resides in the conjunctiva have a chance to invade and cause opportunistic infections.
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