U.S. President Donald Trump on Monday designated a powerful branch of Iran's state military as a terrorist group, ratcheting up already tense relations between Tehran and Washington.

That move, however, "creates another tangle of legislation" that both countries will take years to get through, according to Emily Hawthorne, a Middle East and North Africa analyst at geopolitical intelligence firm Stratfor. Speaking with CNBC's "Squawk Box" on Tuesday, she added that Trump's unprecedented move will make future negotiations with Iran "more difficult."

"The future U.S. government, if they want to negotiate with Iran or negotiate with the Iranian military in any way, they're going to have to take the (Islamic Revolutionary Guard Corps) off of this list," Hawthorne said. "Otherwise, they would be technically negotiating with a terrorist organization."

Set up after the 1979 Iranian Revolution, the Islamic Revolutionary Guards Corp (IRGC) is the elite security arm of Iran's armed forces. It has significant influence in Iran's political system, economy and military.

Monday's decision — set to officially take effect on April 15 — marks the first time the U.S. Department of State has ever labeled a country's state military as a terrorist organization and adds yet another layer of sanctions on Iran.

"The IRGC is the Iranian government's primary means of directing and implementing its global terrorist campaign," Trump said in a White House statement released Monday.