During the fixture against Nottingham Forest on Sunday 24th August, Palace fans unveiled artwork depicting owner Marinakis holding a gun to Morgan Gibbs-White’s head.
The banner came after the England international came close to leaving the side before signing a sudden contract extension, which many supporters believed was down to Marinakis.
A second reason the banner was unveiled was due to tensions at the time, which came when Palace were demoted to the Conference League for breaking UEFA rules on multi-club ownership and Forest quickly took their place in the competition.
“The FA released a statement saying: "Crystal Palace FC has been charged with misconduct in relation to its Premier League fixture against Nottingham Forest FC on Sunday, 24 August.
"It's alleged that the club failed to ensure its spectators and/or supporters (and anyone purporting to be supporters or followers) didn't behave in an improper, offensive, abusive, insulting and/or provocative way during the fixture. Crystal Palace FC has until Tuesday 11 November to provide a response."
Palace fans have blamed Marinakis for fuelling a UEFA investigation into their club's ownership structure, which led to the side dropping to the Conference League. Forest next face Palace in late January and tensions may still be high when the two clubs clash at the City Ground, where Marinakis may attend.