Blues boss Mourinho has been charged for comments he made in the wake of the weekend's 2-1 home defeat to bottom-placed Sunderland, assistant coach Faria was sent to the stands for criticizing the referees after the Black Cats winner and midfielder Ramires allegedly struck Sebastian Larsson with a flailing arm.
FA disciplinary officials have reviewed all of the incidents and decided to charge the trio despite referee Mike Dean taking no action at the time.
"Chelsea midfielder Ramires has been charged by The FA for violent conduct following an off-the-ball incident that was not seen by the match officials but caught on video.
"Rui Faria, Chelsea's assistant manager, has been charged with two counts of misconduct.
"It is alleged that in the 83rd minute of the fixture, Faria used abusive and/or insulting words towards the fourth official (Phil Dowd). It also alleged that Faria's behaviour following the match referee's (Mike Dean) request that he leave the technical area amounted to improper conduct.
"Jose Mourinho has been charged with misconduct in respect of post-match comments he made following the fixture.
"It is alleged that Mourinho's comments constitute improper conduct, in that they call into question the integrity of the referee appointed to the above fixture and/or the integrity of Mr Mike Riley, general manager of the Professional Game Match Officials Limited, and/or the comments bring the game into disrepute."
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