On 29 May 1999, Jonathan was sworn in as Deputy Governor of Bayelsa alongside Diepreye Alamieyeseigha who named in as the governor of the state on the platform of PDP.
On 9 December 2005, Jonathan, who was Deputy Governor at the time, was sworn in as Governor of Bayelsa State upon the impeachment of the current Governor Diepreye Alamieyeseigha by the Bayelsa State Assembly after being charged with money laundering in the United Kingdom.