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UFC legends Jones and 'GSP' frequently top many fans' picks in the long-running debate over the best fighter the combat sport has ever seen.
But Rogan, 53, believes that honour belongs to Johnson and is 'disappointed' that the UFC legend never became a mega-star on the world stage.
"Here's what's disappointing to me, that for whatever reason, 'Mighty Mouse' never became a giant superstar," he said on The Joe Rogan Experience.
"That confused the s**t out of me. When he took Ray Borg and suplexed him and caught him with an armbar on the way down... I was like, 'What the f**k does this guy have to do to become a superstar?' I mean, his skill level is off the chart.
"He doesn't get hit. He's a dazzling fighter. He puts on shows. [Johnson is] the best ever. He's the best, physically, ever."
Johnson, who currently competes with ONE Championship, built an incredible legacy with Dana White's organisation.
'Mighty Mouse' captured the inaugural flyweight championship in 2012 and successfully defended the title 11 times before losing to Henry Cejudo in 2018.
Johnson, 34, last fought against Danny Kingad in 2019 and picked up a unanimous decision victory.
Rogan claimed that the only thing stopping Johnson from "universally" being considered the best of all time is Jones.
"The only thing that keeps him from being thought of as universally the greatest of all time is Jon Jones," he said.
"Jon Jones has been able to beat better guys. Jon Jones fights a better calibre of competition because the 205-pound weight class, at least at one point in time, had a deeper talent pool."
UFC president Dana White has previously said that there is "no debate" over who the MMA GOAT is after naming Jones as his pick.
Featured Image Credit: The Joe Rogan Experience/PA
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