The boxing star was furious when he saw the Paris Saint-Germain star 'cleaning the floor' with the jersey in the Argentina dressing room after their World Cup clash on Saturday.
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Messi could be seen celebrating their 2-0 win over Mexico in footage from the changing room, leading to Alvarez angrily threatening him on social media.
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"Did you guys see Messi cleaning the floor with our jersey and flag," the Mexican boxer tweeted. "He better pray to God that I don't find him. Just like I respect Argentina, he has to respect Mexico!"
Messi's former Argentine teammate Sergio Aguero leapt to his defence, saying: "Mr. Canelo, don't look for excuses or problems, surely you don't know about soccer and what happens in a locker room.
"The shirts are always on the floor after the games are over due to sweat and then if you see well, he makes the movement to remove the boot and accidentally hits it."
Cesc Fabregas also defended him, telling Alvarez: "You neither know the person, nor do you understand how a locker room works or what happens after a game.
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"All t-shirts, even the ones we wear ourselves, go on the floor and are washed afterwards. And more when you celebrate an important victory."
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But while Alvarez remained angry on the Mexico squad's behalf, veteran player Guardado didn't appear to be fussed.
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It was the 36-year-old's shirt that was apparently kicked in the dressing room, but speaking at his fifth World Cup for his country, the veteran says he knows Messi wasn't being disrespectful.
Speaking to Argentinian broadcaster TyC Sports, Guardado said: I know the person Messi is.
"It's a deal with the staff that when it's all sweaty, it gets left on the floor. Be it your jersey or rival.
"Canelo doesn't know what a dressing room is. It seems silly to me. That shirt was mine, I exchanged it with Leo."