Guardiola, who has always been outspoken on the Catalan issue, donned a yellow ribbon to show solidarity with imprisoned Catalan politicians.
In December, Guardiola spoke out about his wearing of the symbol: "To make a rebellion on something like that, you have to be something tough to be in prison. And they are still there. So, while they are not out, always here (points to ribbon) will be shared with me. Because, OK, they can suspend me for doing that, but the other people are in jail. If they want to suspend me - UEFA, Premier League, Fifa - it’s OK."
The FA said in a statement "Pep Guardiola has been charged for wearing a political message, specifically a yellow ribbon, in breach of The FA’s kit and advertising regulations."
The Catalan born Man City manager has until 6pm on Monday 5th March to respond to the charge.