In 2002, Sophocleus entered the Alabama gubernatorial race on the Libertarian Party of Alabama's ticket against incumbent Don Siegelman and previous opponent Bob Riley. In the 2002 race, which was one of the closest in Alabama's history, Sophocleus received 23,242 votes (~2%),[4] a number which was greater than the margin of victory in the race.
The only reason the governor's race in Alabama was so close this year as to be disputed beyond election night was that the Libertarian candidate, John Sophocleus, attracted 23,000 votes.[5][6]
On 8 June 2006, in the wake of Stephen P. Gordon's acceptance of a position with the national Libertarian Party and subsequent resignation from the LPA Executive Committee, Sophocleus was named Vice-Chairman of the Libertarian Party of Alabama.[7]
Beginning in 1998, Sophocleus was involved in litigation[9] with the State of Alabama, the Alabama Department of Transportation, and others over the eminent domain seizure of his US Highway 280 home, near The Bottle, Alabama. Sophocleus contended that the state acted improperly by evicting him and allowing highway workers to live in his house for several months (while he still held legal title to the home) rather than immediately demolishing it as was stated would happen in United States district court.