This study aimed to evaluate the bacterial flora in the conjunctival fornix of clinically normal Persian squirrels (Sciurus anomalus). Forty healthy Persian squirrels of equal gender distribution with similar ages (approximately 2 yr) were used for this study. A total of 80 conjunctival swabs were taken from both the right and left eyes of each squirrel for aerobic and anaerobic bacterial identification. A slit-lamp examination was conducted and no external ocular disease was identified. From 80 normal eyes, Staphylococcus spp. comprised the most frequently isolated organism (83%), while Corynebacterium spp. were the second most frequently isolated bacteria (56%), followed by Streptococcus spp. (53%), Chlamydia spp. (33%). Mycoplasma spp. (30%), Pseudomonas spp. (23%), Escherichia coli spp. (12.5%), Enterococcus spp. (7%), and Micrococcus spp. (4%) were also isolated. The most frequently isolated bacteria from the conjunctival fornix of healthy Persian squirrels were Staphylococcus spp. followed by Corynebacterium spp.