The former Monaco playmaker tweeted and compared an image of a young Mendy to a character on a packet of Conquitos, a well-known sweet brand available in Portugal.
After a swift backlash from fans on twitter, the Portuguese midfielder deleted the tweet and posted a second tweet which said, "Can't even joke with a friend these days... You Guys..."
The 25-year-old’s tweet is alleged to have committed “aggravated breach” of FA rules and has until 9th October, 2019 to respond.
Many organizations have condemned the act including Football anti-discriminatory body ‘Kick It Out’ as they urged the FA to act accordingly, adding that "racist stereotypes are never acceptable as 'banter'"
Silva has written to the FA to say he regrets his actions but could face a six-match ban if found guilty.
In a statement on Wednesday the governing body said: “Bernardo Silva has been charged with misconduct for a breach of FA Rule E3 in relation to a social media post on September 22, 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.
"The midfielder has until 9 October 2019 to provide a response."
Team-mate Raheem Sterling and club coach Pep Guardiola have come out to defend Silva over the tweet.
Mendy has also written to the FA to defend Silva, who he played with at Monaco before joining Manchester City together in 2017.
