Chelsea defender Marcos Alonso has been charged with violent conduct over an apparent stamp on Southampton striker Shane Long when the sides met at St Mary's.
The incident went unpunished during the match, which the Blues won 3-2, but the FA has chosen to take retrospective action after reviewing video footage.
Alonso has until 6pm on Wednesday to respond to the charge, which could result in a three-match ban.
Saints manager Mark Hughes has spoken out against the challenge, dubbing it a "dangerous tackle" and arguing that it could have broken Long's leg.
Chelsea boss Antonio Conte has been urged to speak to the defender about the tackle.