Guardiola was born in Catalonia and is revered in the region because of his links with Barcelona's soccer team, as a player and coach.
Guardiola has been wearing the yellow ribbon at matches and news conferences since Catalonia's failed secession bid in October when a banned independence referendum was held.
It is unclear why the FA has waited until now to charge Guardiola.
The English FA says the ribbon is a "political message" which requires him to be charged with being in breach of kit and advertising regulations.
Guardiola has until March 5 to respond to the charge.
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