Wenger has until 6pm on Friday to respond, but refutes the charge.
Wenger is contesting the FA charge. Nothing has changed. I've been in England for 21 years and I've tried to serve this game with honesty, integrity and when I have something to say, I say it.
Winger Eden Hazard and midfielder Cesc Fabregas were rested during Chelsea's convincing 5-0 Premier League win over Stoke City on Saturday, with both replacements Danny Drinkwater and Willian scoring. Gunners boss Arsene Wenger called the decision to award a penalty "farcical."
Wenger was speaking after a pulsating and at times controversial 2-2 draw with Chelsea at the Emirates Stadium.
"At the moment we have to face surprising decisions", Wenger added.
However, Hector Bellerin - having earlier fouled Hazard for the penalty - popped up with an injury time equaliser.
Arsenal manager Wenger given touchline ban, fine for referee incident
Alonso snatched what he thought was the victor six minutes from time, but Arsenal showed great resolve to push for an equaliser and Bellerin atoned in the 92nd minute with a stunning half-volley from the edge of the area.
When asked for their thoughts on the penalty award, Bellerin said: "He's always very quick in the box".
"We can only continue to play the way we want to play, and hope at one stage things will go for us". We will have to watch the replay to see what really happened. I haven't scored in a while so it was great to do it for our comeback.
"I never had that much dairy anyway and the few times I've had it in the team hotel I've had an upset stomach".
"Then we could have lost the game but we had the resources to come back, and in the end maybe it's a fair result".