Background: To compare iodine-125 ( 125 I) with ruthenium-106 ( 106 Ru) episcleral plaque radiation therapy in terms of the effectiveness and non-inferiority for choroidal melanoma treatment.Objective: To report the non-inferiority of new made iodine-125 ( 125 I) compared with ruthenium-106 ( 106 Ru) episcleral plaque radiation. Patients and Methods: A retrospective, non-randomized comparative case series. In this series the patients treated with 125 I and 106 Ru episcleral plaques for choroidal melanoma between September 2013 and August 2017 at Farabi Hospital are compared. Local control of choroidal melanomas after 125 I and 106 Ru plaques implantation and vision changes are the main outcome measures. Results: A total of 35 patients were identified ( 125 I = 15, 106 Ru = 20). No significant difference between two groups in visual acuity, diameter and thickness changes were observed after treatment. Multivariate linear regression (MLR) analysis showed that final diameter was only, independently and significantly, correlated with the pre-treatment diameter of the tumor (β = 0.59, 95% confidence interval [CI]: 0.29, 1.34, P = 0.003). The same MLR analysis for the final thickness and visual acuity, after adjusting for age and sex showed no significant difference between two groups. A single patient treated with 106 Ru had local tumor recurrence with no one in the 125 I group. No statistical difference in the rate of ocular complications was observed. Conclusion: The treatment with our 125 I plaques is as effective as 106 Ru plaques in controlling choroidal melanoma tumor and preserving the vision during the two and half year of follow-up. The complication rates are alike. It means that the effectiveness of 125 I is not only comparable to 106 Ru but also superior when the outcome of the interest is the thickness of the tumors.