Normal fungal conjunctiva microbiota of horses remains stable in healthy animals, free from ocular and/or systemic diseases which may, eventually, cause ocular alterations. The knowledge of the fungal microbiota is of great importance due to the reduced number of studies reported in the literature and also to the large occurrence of ocular alterations, mainly keratomycosis, in these animals. The aim of this study was to isolate and to identify the fungi present in the ocular conjunctiva of healthy horses belonging to the Military Police Cavalry of Alagoas. Samples from both conjunctival sacks from 50 horses were taken using a sterile swab and submitted to fungal cultures. These samples were seeded by radial spreading of the swabs on the Sabouraud agar surface with chloramphenicol, at a concentration of 50mg/L, in Petri dishes. Next, dishes were incubated at room temperature (± 28ºC) for 15 days. Horses conjunctival fungal microbiota was found to be composed by Aspergillus spp. (62%), Microsporum gypseum (6%), Penicillium spp. (6%), Curvularia spp. (5%), Candida spp. (3%), Fusarium spp. (3%), Acremonium spp. (2%), Bipolaris sp. (1%), Cladosporium sp. (1%), Chrysosporium sp. (1%), Rhodotorula sp. (1%), Aureobasidium sp. (1%) and Scopulariopsis sp. (1%). There is a wide variety of yeast-like and filamentous fungi colonizing the clinically healthy horses' ocular conjunctiva, out of which Aspergillus sp. is predominant. Although this was a straightforward study and have not recorded any ocular lesions that suggest fungi infections, these fungi might eventually be involved in this type of ocular pathology for the studied species.