Wigan Athletic and Bolton Wanderers have been charged following a mass confrontation at the end of their League One fixture on 27 February.
Tempers flared at full-time with both sides clashing, leading to an FA charge for failing to ensure their players did not behave in an improper way.
The clubs have until Wednesday to respond to the charge.
The defeat was a blow to Bolton’s promotion hopes, leaving them third in the League One table and level on points with second-placed Derby County.
Wigan’s victory was their second over Bolton in the league this season, having also beaten Wanderers 4-0 away from home in August.
