Colbert went off script, saying, "'Thank you?' F*ck You!" which led to raucous applause and cheering from the audience.
"Why the hell would he do this?" he wondered. "This isn't even one of his campaign promises," noting that during the campaign, Trump tweeted: "Thank you to the LGBT community! I will fight for you while Hillary brings in more people that will threaten our freedoms and beliefs."
"What the hell does he think the 'T' in LGBT stands for?" Colbert asked, exasperated. "Trump? Tomato?"
Colbert then addressed Caitlyn Jenner, who seemed surprised by Trump's decree, saying, "Caitlyn. I don't know if I'm the first person to break this to you, but he's a liar."
"I know he said he was your friend, but he was using you girl. You deserve better," he continued.
Colbert then noted that the 15,000 trans troops were not only fired by tweet, but they were fired "by a rich guy who, during Vietnam, sidestepped the draft with four deferments and a medical disqualification for bone spurs in his foot."
He finished off by speculating that Trump was distracting everyone with the ban because "'Repeal & Replace' is getting 'a** & kicked.'"