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The two have very different styles. Mayweather is a defensive virtuoso, capable of sliding around and avoiding big hits from opponents. Pacquiao uses a quirky combination of speed, power, and angles to deliver big hits.
In a post-fight video interview with Fight Hype, Mayweather described what makes Pacquiao so tough to fight, pointing out his his left-handedness and ability to "set traps" and unload shots on opponents:
"He's a good fighter. He's a hell of a fighter. And he'll beat a lot of fighters 'cause, the way he fights, he basically sets a trap. He sets traps for other fighters to where he can load up all of his arsenal and use different angles to win on fighters."
When asked how he studied Pacquiao's style, Mayweather said he did it through sparring, and then gave a detailed scouting report of what Pacquiao does in the ring:
"He throws the awkward left, a straight left hand, leans and throws it, and bobbing and weaving, bobbing and weaving, keep pressure, keep pressure. When he gets the guy, he goes crazy drilling him, drilling him. And the guy opens, Pacquiao throws the one shot and then he catches the guy. And that's what he do."
In another video interview with Fight Hype, Mayweather noted Pacquiao's left hand has "a little thump" unlike any other boxer he's fought.
Mayweather's defensive skill helped him avoid some of the Pacquiao hits that have devastated opponents in the ring.
In a 2008 fight with Oscar De La Hoya when Pacquiao was rising to the top of the boxing world, he hit De La Hoya with a brutal straight left hand that Mayweather describes:
In a 2010 fight with Antonio Margarito, Pacquiao showed off his speed and power, unleashing a dazzling combination when Margarito opened up, also like Mayweather described:
Pacquiao was able to open up Mayweather occasionally, hitting him with a one particularly strong straight left hand:
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However, Mayweather guarded himself from Pacquiao's blitzing combinations, and that may have been the biggest difference in the fight. Mayweather simply covered up and let Pacquiao throw combinations that didn't land or lead to any holes:
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Though Pacquiao fought with an injured shoulder, it seems Mayweather was simply better prepared. He clearly knew what Pacquiao wanted to do, and he guarded himself, not allowing Pacquiao to use his greatest strengths.