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The county seat of Owyhee County is Murphy, and its largest city is Homedale. Owyhee County's history is inextricably linked to the mining boom that dominated Idaho Territory in the second half of the 19th Century. Silver City and Ruby City are among the state's most noteworthy ghost towns from the period. At its height in the 1880s, Owyhee County was among the most populous places in Idaho. Today it is among the least populous.
Nearly all of the county is high intermountain desert, with plentiful sagebrush and basalt canyons. The Owyhee Mountains in the west dominate the landscape, with Hayden Peak reaching 8,403 feet above sea level. The lowest elevation is at the county's northwest corner, where the Snake River is just above 2,000 feet at the Oregon border. The Snake forms most of the county's northern border from Oregon to just west of Glenns Ferry in Elmore County.
A tributary of the Snake is the Bruneau River, which flows north from Nevada through the eastern section of the county. The Owyhee River starts in the southwestern part of the county and flows westward into Oregon; it eventually enters the Snake at the state border south of Nyssa. Needless to say, fishing opportunities abound.