Spurs caretaker manager Christian Stellini and Brighton coach Roberto De Zerbi were sent off in the 58th minute following a brawl involving both benches.
“Tottenham Hotspur and Brighton & Hove Albion have been charged for a mass confrontation that took place during the 58th minute of their Premier League game on Saturday 8 April,” read a statement from the FA on Wednesday.
“It’s alleged that both clubs failed to ensure their technical area occupants conducted themselves in an orderly fashion and/or do not behave in a way which is improper. Tottenham Hotspur and Brighton & Hove Albion have until Monday 18 April to respond.”
The clubs have until April 17 to respond to the charges.
The game was notable for a number of controversial decisions by the officials, with Brighton twice having goals disallowed by the VAR for handball, while they were denied a penalty by Atwell for a Pierre-Emile Hojbjerg trip on Kaoru Mitoma.