Objective: To evaluate seasonal effects on the presence or absence of fungal and aerobic bacterial flora of the conjunctival fornix of normal Florida Thoroughbred horses. Sample population: Both eyes of 100 horses. Procedure: Horses with normal anterior segment ophthalmic examinations from three farms in north central Florida were included. Each animal had the ventral conjunctival fornix of each eye swabbed with sterile culturettes. Samples were taken in October, January, April, and July (1999-2000). Aerobic and fungal cultures were plated. Bacterial cultures were reviewed at 24 and 48 h. Fungal cultures were reviewed weekly for 4 weeks. Logistic regression analysis with season as a factor and age of the horse as a covariate was performed. Statistical significance was set at P < 0.01. Results: Horses ranged from 3 to 24 years of age, with a median age of 9 years. Twenty-four genera of bacteria and 35 genera of fungi were recovered. Corynebacterium sp., Staphylococcus sp., Bacillus sp. and Moraxella sp. were the bacteria most frequently isolated. Mold species, dematiaceous mold species, Chrysosporium sp., Cladosporium sp., and Aspergillus sp. were the most frequently recovered fungi. Season did not have a significant effect on the presence of microorganisms isolated for individual horses adjusted for age. Younger horses had an increased incidence of gram-negative rods and fungal isolates. The number of bacteria and fungi isolated are not uniform across seasons. Conclusion: There were no significant differences between the number or type of organisms cultured during the sampling seasons in normal Florida horses. A large range of normal bacterial and fungal flora were isolated from these horses. The number of bacteria and fungi isolated are not uniform across seasons. The likelihood of detecting an organism depends on the horses' age.