Silva posted a tweet that appeared to compare Mendy's likeness to a cartoon character who features on the packaging of Conguitos, a brand of chocolate bar in Spain.
A statement from the FA read: "Bernardo Silva has been charged with misconduct for a breach of FA Rule E3 in relation to a social media post on 22 September 2019.
"It is alleged that the Manchester City player's activity breaches FA Rule E3(1) as it was insulting and/or improper and/or brought the game into disrepute.
"It is further alleged that the activity constitutes an "Aggravated Breach", which is defined in FA Rule E3(2), as it included reference, whether expressed or implied, to race and/or colour and/or ethnic origin."
Sources have told ESPN that as well as the tweet, the FA also looked at a video Silva posted of Mendy on Instagram in 2018.
Silva, 25, defended his actions and said: "Can't even joke with a friend these days... you guys," but anti-racism body Kick It Out condemned the initial tweet, saying racist stereotypes are never acceptable.
Manchester City manager Pep Guardiola has also defended Silva, saying: "If something happens it will be a mistake because Bernardo is an exceptional person.
"Bernardo is one of the loveliest people I've met in my life. He speaks four or five languages -- that's the best way to understand how open-minded he is.
"One of his best friends is Mendy. He's like a brother. He took a picture of Benjamin when he was young and related it with this cartoon, quite similar for the image."
A player found guilty of discrimination while on the field of play faces an automatic six-match ban. Silva's case is different as discrimination on social media does not trigger the same punishment if found guilty.
An independent regulatory commission will hear any case, with Silva obliged to respond to the charge by Oct. 9.