Conjunctival melanoma patients often follow an unpredictable course with significant rates of recurrence and metastases despite optimal treatment. Can we better understand conjunctival melanomas by applying the cancer stem cell hypothesis? The cancer stem cell hypothesis posits that cancers exist as a hierarchical system where cancer stem cells generate and maintain tumors. Targeting cancer stem cells may be the key to future treatments. Directed treatments need to focus on key differences between cancer stem cells and normal tissue stem cells. These directed treatments may lead to curative therapies and decrease the number of recurrences and metastases.