This report aimed to discuss two nearly identical cases of primary conjunctival mucosa-associated lymphoid tissue (MALT) lymphoma mimicking allergic conjunctivitis. Two patients were referred to the Department of Ophthalmology, Ilsan Paik Hospital, Inje University because of the intractability to conventional treatment for initially diagnosed allergic conjunctivitis. On ocular examinations, normally pigmented, giant papillae-like lesions were found in the bilateral upper conjunctivae. Excisional biopsies were performed. Histopathologic and immunohistochemical examinations of the conjunctival biopsies revealed MALT lymphoma in both patients. The patients subsequently received radiation therapy and achieved complete remission with no evidence of recurrence during the follow-up periods of 13 and 11 months, respectively. Ophthalmologists should be reminded that a primary conjunctival low-grade malignant lymphoma may masquerade as allergic conjunctivitis with similar clinical features.