Doniphan County (county code DP) is a county located in the U.S. state of Kansas. As of the 2010 census, the county population was 7,945. Its county seat is Troy, and its most populous city is Wathena.Doniphan County is included in the St. Joseph, MO-KS Metropolitan Statistical Area, which is also included in the Kansas City-Overland Park-Kansas City, MO-KS Combined Statistical Area.