The charges relate to incidents during Blackburn's Worthington Cup quarter final game with Wigan at the JJB Stadium when Souness was sent from the dug-out after an altercation with fourth official Matt Messias.
An FA statement read: "We can confirm that the FA has today charged Blackburn Rovers manager Graeme Souness with improper conduct (FA Rule E1) and abusive and/or insulting language to match officials (FA Rule E2). "These charges relate to an incident during Blackburn's Worthington Cup match away to Wigan Athletic on 17th December 2002. "He has 14 days to respond to the charges."