Estrogenic activity-oriented fractionation and purification of methanol extract from the rhizome of Cyperus rotundus, a well-known traditional herbal medicine, led to the isolation of six sesquiterpenes. 4α,5α-Oxidoeudesm-11-en-3-one (2) and cyper-11-ene-3,4-dione (3) together with four known sesquiterpenes, cyperotundone (1), caryophyllene α-oxide (4), α-cyperone (5), and isocyperol (6) were obtained from the hexane and dichloromethane fractions. Compounds 2 and 3 were newly isolated from natural resources in particular. To identify the possible use of isolated compounds as an alternative to hormone replacement therapy (HRT), estrogenic activity was evaluated by E-screen assay on MCF-7 BUS cells. Among the all isolated compounds from the rhizome of Cyperus rotundus, newly isolated from natural resource, 2 exhibited the most potent estrogenic activity. In an estrogen sensitive reporter gene assay, 2 significantly increased transcriptional activities. As a phytoestrogen, 2 was assessed by investigating dual action on ER-α and ER-β in competitive binding assay. It was found that 2 exerted higher binding affinity to ER-β than ER-α and it also showed both estrogenic and antiestrogenic effects depending on the E₂ concentration. Our results indicate that newly isolated from Cyperus rotundus, 2 has biphasic activities on estrogen receptors which could be useful as an alternative HRT.