The charge relates to an incident close to the end of their Barclays Premier League fixture at the Liberty Stadium last Monday, in which there was a fracas involving Hull's Tom Huddlestone and Yannick Sagbo and Swansea's Ashley Williams. Chico Flores then flung himself to the ground feigning that Sagbo had elbowed him.
A statement on the FA's official website said: "Both Swansea City and Hull City have been charged by the FA in that they failed to ensure their players conducted themselves in an orderly fashion in or around the 80th minute of their fixture on December 9, 2013.
"The clubs have until 6pm on December 17, 2013 to respond to the charge."
The match ended in a 1-1 draw after Danny Graham's opener against his former club was cancelled out by Flores in the 60th minute.
Sagbo and Williams were both booked after the incident following an altercation, while Swansea midfielder Jonjo Shelvey was also shown a yellow card in the aftermath.
The game had been the first Premier League match between the two sides.