Purpose: To determine the association between conjunctival epithelial Dysplasia (squamous intraepithelial neoplasia) and its melanosis (microscopic non-proliferative melanin pigmentation) in conjunctival biopsies. Methods: In this retrospective case series, histopathological slides from all conjunctival biopsies obtained in Khalil Hospital affiliated with Shiraz University of Medical Sciences for a period of 6 years (April 2009– July 2015) were reviewed. After considering the exclusion criteria (nonmelanotic pigmentation, melanocytic proliferations, and squamous cell carcinoma), conjunctival biopsies were divided histopathologically into two groups of dysplastic and non-dysplastic. Then, the slides were reviewed by one ophthalmopathologists and one general pathologist. Melanin pigmentation was recorded in both groups as 0, 1+, 2+, and 3+. The data were analyzed, and the groups were compared. Results: Overall, 685 cases with a mean age of 47. 78 (± 17. 74) years were included in this study. Dysplastic and non-dysplastic groups comprised 135 (19. 7%) and 550 (80. 3%) specimens, respectively. Seventy‑ six percent (76%) of the specimens in the dysplastic group versus 40% in the non-dysplastic group had melanosis (P = 0. 001). However, the degree of Dysplasia (1+, 2+, and 3+) was not statistically correlated with the degree of melanosis (1+, 2+, and 3+) (P = 0. 393). Conclusion: Our results demonstrated that melanosis is a common finding in conjunctival epithelial Dysplasia and might indicate an association with conjunctival epithelial Dysplasia.