Encephalitozoon cuniculi was first recognized as the disease agent in rabbits in 1922. The genotype of E. cuniculi isolated from laboratoryrabbits with the neurologic disease was described as genotype I. In the eye, this parasite causes damage to the lens, causing phacoclasticuveitis and cataracts. Intraocular infection often occurs in cases of transplacental transmission. There has been no report on the moleculardiagnosis of the parasite in Turkey. The current study is the first report on the detection of E. cuniculi spores using the molecular methodin Turkey. In our previous study, a rabbit breeding facility was determined seropositive for E. cuniculi infection monitored for five yearsin terms of clinical symptoms. An autopsy was performed for a definite diagnosis of the infection. Samples were stained according tothe hematoxylin-eosin (H&E) staining after tissue processing procedure and histopathologic analysis was performed. In addition to,the samples for DNA extraction were also taken during the autopsy. ECUNF and ECUNR species-specific primer pairs were used foramplification and genotyping of E. cuniculi. The animals were observed no clinical symptoms except ocular lesion (n=9). Therefore, oneof these rabbits was used in the autopsy to definite diagnosis and determination of the damage to the eye. As histopathological, thelesions in the eye were found in the initial or middle stage of progressive infection. The DNA sequence showed that E. cuniculi examinedin the present study were genotype I. Possible cause of the visible white mass in the rabbit’s eye may be the parasite infection. Therefore,clinicians may consider E. cuniculi as one of the possible causes of ocular lesions in rabbits during daily inspection or ophthalmologicalexamination.