Hughes Mountain and the Hughes Mountain State Natural Area are located in southern Washington County, Missouri (Sections 28 and 33, T36N R3E) just south of the Big River and Highway M on Cedar Creek Road in the St. Francois Mountains range of The Ozarks. The mountain reaches an elevation of just over 1,200 feet, rising 430 feet above the Big River. The Hughes Mountain Natural Area of the Missouri Department of Conservation encompasses of the mountain, including the rhyolite glade at its top.