A brawl broke out between the two sets of players after Martial Godo was accused of provoking the Bolton fans behind the goal.
A statement on the official FA Spokesperson account read: “Wigan Athletic and Bolton Wanderers have been charged following a mass confrontation at their EFL League One match on Tuesday, February 27.
“It is claimed that both teams failed to ensure that their players did not engage in inappropriate and/or provocative behavior following the final whistle.
“Wigan Athletic and Bolton Wanderers both have until Wednesday, March 6 to provide their responses.”
Wigan won 1-0 on the night, with Stephen Humphrys scoring the crucial goal in the second half.
After the game, Ian Evatt stated, “Godo was sprinting almost the entire length of our fans with his hands to his ears. He was goading them, which is wrong, and we will not take it.
“They probably deserved to celebrate in front of their own fans because of the amount they ran in that game but they shouldn’t be doing that to our supporters, it isn’t right.”