Endometriosis is an enigmatic disease characterized by the presence and growth of endometrial-like tissue outside the uterine cavity. The etiology of endometriosis is poorly understood, yet recent evidence suggests that epigenetic aberrations and heritable changes in the genome may be the key to understanding how to approach this disease. Difficulty in long-term management of endometriosis symptoms and unpredictability of treatment outcome necessitate research into other treatment modalities, such as Western herbal medicine. This article reviews commonly used herbs in the treatment of endometriosis, the effects of phytochemical constituents on endometrial cells, and the impact on the epigenome.