Sir Alex Ferguson has been charged with using abusive and/or insulting words towards referee Mark Clattenburg.
The FA confirmed in a statement on their website that "the charge relates to Ferguson's conduct at halt-time" during the Bolton match.
The United boss was unhappy with what he claimed was a lack of protection for his players during the recent 1-0 defeat at the Reebok Stadium on Saturday.
Sir Alex was sent to the stands for the second half of the match.
He has until 11 December to respond to the charge, and if found guilty could face a fine and potentially a touchline ban.