The social media post compared Mendy with the mascot of Spanish confectionery brand Conguitos and was quickly condemned by Kick It Out and anti-discrimination groups.
Despite Pep Guardiola’s repeated defence of the midfielder, the Manchester City midfielder could potentially face up to a six-game ban.
A statement released by 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.
“The midfielder has until 9 October 2019 to provide a response.”
On the same day as the tweet, Silva posted: "Can't even joke with a friend these days... You guys..."
It is understood Silva wrote to the FA to express regret over the Mendy tweet, while Mendy also wrote to the governing body to say that no personal offence had been caused.
City manager Pep Guardiola also leapt to the defence of his player.
"Bernardo is one of the most lovely people I have ever met in my life," Guardiola said last week. "He speaks four or five languages - that is the best way to understand how open-minded he is - and one of his best friends is Mendy. He is like a brother for him. The image for the two is not about the colour of the skin."
Additional reporting by PA
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