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Flake, R-Ariz., was at a tax reform event in Mesa, Arizona on Friday night when he was caught bashing the president in a conversation with friend, Mesa Mayor John Giles.
"If we become the party of Roy Moore and Donald Trump, we are toast," Flake was caught saying by ABC affiliate KNXV.
Moore is running for the vacant Senate seat in Alabama left by Attorney General Jeff Sessions. He has come under fire for a number of allegations of sexual harassment and assault, but has refused to leave the race.
Trump is a frequent opponent for Flake, who announced last month he would not seek re-election in 2018 in a fiery speech condemning the president from the floor of the Senate.
Flake indirectly called out Trump in his Senate speech, saying, "We must dedicate ourselves to making sure that the anomalies never becomes the normal, with respect and humility."
He told ABC News' Mary Bruce of Moore in a Nov. 9 interview on Capitol Hill, "If there is any shred of truth to these stories, he ought to step aside. And now."
Flake's criticism of Trump and the GOP weren't the only interesting comments to be caught on the live mic Friday night.
Giles was caught appearing to encourage Flake to run for president in 2020.
"I am not throwing smoke at you, but you are the guy -- just for fun, think about how much fun it would be -- just to be the foil, you know, and point out what an idiot this guy is," Giles said, apparently referring to Trump. "Anyway, I hope you do it."
Giles, who is a moderate Republican like Flake, has been mayor of Mesa since 2014.