Alonso appeared to stand on the back of Southampton striker Long's calf in the first half as his team trailed 2-0 on Saturday.
"There is one thing in his mind there, and that is to hurt Shane Long and Mike Dean is looking right at the incident".
If that is the case, a three independent panellists then individually rule on whether Alonso's tackle warranted a red card and, if the decision is unanimous, an FA charge can be brought.
An FA statement read: "Chelsea's Marcos Alonso has been charged with violent conduct following an incident with Southampton's Shane Long".
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"It happened in the 43rd minute of Saturday's game. and was not seen by the match officials but caught on video".
The incident was not seen by the match officials but the FA have chose to take retrospective action after reviewing footage.
Southampton boss Mark Hughes was disapproving of the tackle at the time.
According to the Daily Mail, FA Chiefs are still investigating the challenge and are reviewing footage of the incident.
"The disappointment was the officials didn't see it".