Reading and Sheffield United have been charged with failing to control their players and/or officials after incidents during Saturday's Premiership fixture, while Royals coach Wally Downes has been charged with improper conduct.
Blades boss Neil Warnock, who angered Downes with a stamping gesture which was apparently mis-interpreted, has been given a warning but will not face any formal disciplinary action.
United winger Keith Gillespie faces up to two months on the sidelines after admitting to a charge of violent conduct earlier today.
An FA statement said: 'Both clubs have been charged with failing to control their players and/or officials. This charge relates to a mass confrontation on the touchline in the second half of the match on 20 January.
'Reading coach Wally Downes has been charged with improper conduct in relation to the same incident.
'Sheffield United manager Neil Warnock has been reminded of his responsibilities but will not face any formal disciplinary action.
'Reading, Sheffield United and Downes have until February 7 to respond to the charges.'
Gillespie will have a personal hearing with a disciplinary commission on Tuesday.
Yesterday he was charged by the Football Association in relation to an incident with Reading midfielder Stephen Hunt during United's 3-1 defeat at the Madejski Stadium.
Gillespie had already been dismissed moments earlier by referee Mark Halsey for elbowing Hunt just seconds after his arrival as a substitute.
As the former Northern Ireland winger made his way off the pitch, he again confronted Hunt and appeared to hit him in the face.
In accepting the charge, and ahead of his disciplinary hearing, Gillespie faces the prospect of a six-match suspension which would see him ruled out until the end of March.
Gillespie is already banned for United's next three matches for the initial red card and misses next Tuesday's home date with Fulham, the match at Blackburn on February 3 and the Bramall Lane clash with Spurs a week later.
The FA have the power to impose a further three-match penalty on the 31-year-old for the second infringement, which would see him miss games at Liverpool and Chelsea on February 24 and March 17 respectively, sandwiched by a home date with Everton on March 3.
The fact manager Neil Warnock's side are out of the FA Cup and there is an international break on March 24 compounds Gillespie's problems, with a return only possible on March 31 at Bolton.
Given the threat of such a lengthy suspension, it means any hope Gillespie had of a move away from United this month after handing in a transfer request at the weekend, is almost non-existent.