The boss of the rock-bottom Potters was sent to the stands as he lashed out during the first half of the crushing loss.
Marko Arnautovic’s booking for simulation by referee Jon Moss led to him seeing red, as it came seconds after Hughes felt his side should have had a foul when Dele Alli sent Jon Walters sprawling.
Hughes left the technical area to go and vent his fury at assistant ref Peter Kirkup before he then got involved in a war of words with fourth official Jon Moss.
He then turned his anger to the visiting Spurs supporters, mouthing off at the away fans as they taunted him as he stormed down the tunnel.
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An FA statement on Tuesday said: “Mark Hughes has been charged with misconduct following Stoke City’s game against Tottenham Hotspur on Saturday [10 September 2016].
“It is alleged that his behaviour in or around the 34th minute of the fixture amounted to improper conduct.
“He has until 6pm on 16 September 2016 to respond to the charge.”
Following the weekend’s game, Hughes attempted to explain his actions.
When asked why he felt he had been sent to the stands, Hughes said: “I came out of my technical area.
“I was upset and felt the assistant referee hadn’t flagged for a clear foul. The referee then thought it was the right decision to book Marko when he was just trying to take evasive action.
“Two decisions I thought should have gone our way so I reacted in a forceful manner. When you come out of your technical area, it’s not allowed – sometimes you forget that.
“Mr Moss, bless him, decided that warranted a sending off, which, by the letter of the law it did. So I have to hold my hands up.”