A survey was carried out to describe the normal aerobic bacterial flora of the conjunctiva and nasal cavity of captive houbara bustards (Chlamydotis undulata), kori bustards (Ardeotis kori), and white-bellied bustards (Eupodotis senegalensis) maintained at the National Avian Research Center, Abu Dhabi, United Arab Emirates. A total of 58 samples were examined from the nasal cavity and 55 samples from the conjunctiva of healthy bustards. There was no bacterial growth in 45% of conjunctival samples. Bacteria isolated from the conjunctiva of healthy birds included Micrococcus spp., Staphylococcus auricularis, Staphylococcus xylosus, Staphylococcus capitis, Staphylococcus warneri, Bacillus spp., and Enterobacter amigenus. Bacteria isolated from the nasal cavity of healthy birds included Bacillus spp., Micrococcus spp., S. auricularis, S. xylosus, Staphylococcus simulans, Staphylococcus saprophyticus, Staphylococcus hyicus, Staphylococcus cohnii, Staphylococcus sciuri, Aerococcus spp., and Providencia rettgeri. These findings were compared with bacterial isolates from bustards with clinical signs of ocular or upper respiratory tract diseases. Mycoplasma spp., Pseudomonas aeruginosa, Pseudomonas stutzeri, Proteus mirabilis, Escherichia coli, Klebsiella spp., Aeromonas hydrophila, and Staphylococcus aureus were the pathogenic bacteria isolated from the conjunctiva of 34.3% bustards with ocular discharges. Mycoplasma spp., P. aeruginosa, Pseudomonas spp., P. mirabilis, E. coli, Klebsiella pneumoniae, and S. aureus were the pathogenic bacteria isolated from the nasal cavity of 74% bustards with upper respiratory tract diseases.