The tweet sparked accusations against him for being a racial stereotype.
Bernardo also faces a possible ban from the game in case proven guilty, as the defending champions are already off to a troubled start to the season.
Here is more.
Bernardo's controversial tweet draws anti-racism campaigners' attention
A few days back, Bernardo had posted an image of Mendy, representing him as a child, alongside the picture of a mascot of a chocolate peanut butter brand of Spain.
The tweet was objected by many, as several anti-racism campaigners, including Kick it Out, condemned it.
Following an uproar on social media, Bernardo later deleted the tweet.
FA charges Bernardo for having committed "aggravated breach"
Meanwhile, the FA has charged Bernardo of committing an "aggravated breach", not just regarding an improper social media post, but also referencing to Mendy's "race and/or color and/or ethnic origin".
He has until October 9 to respond to his actions and could be banned upon proven guilty, asides being sent for an education course on the same.
Mendy defends Bernardo's tweet as a joke
Meanwhile, Mendy has defended Bernardo, as he has written a personal letter to the FA, stating regret of any harm caused by the latter's tweet unintentionally, and dismissed the tweet as a joke.
After Bernardo had deleted the tweet, he followed it up with a message, saying, "Can't even joke with a friend these days."
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Pep Guardiola defends Bernardo's tweet as a joke
"He is not absolutely guilty because of his intention ... it was just a joke. It's a cartoon and the face is quite similar. The same happened a thousand million times with white people. It's the same," said City's manager Pep Guardiola in Bernardo's support.
Bernardo faces six-match ban amidst City's injury crisis
As the FA awaits Bernardo's response to their charge, it is being assumed that he is likely to get a ban of a maximum of six matches.
Meanwhile, City are going through a rough patch, along with injuries, which has ruled out top players like Aymeric Laporte, Leroy Sane and John Stones.
City are currently second in the Premier League, five points behind Liverpool.