By Sue Pleming
Obama's comments came as thousands of Mousavi supporters took to the streets in Tehran for a fourth day of protests over Friday's disputed Iranian presidential elections.
So far, Obama has been cautious in opining about the candidates, telling reporters earlier on Tuesday he did not want to be seen as "meddling" in Iranian internal affairs.
But in a television interview later on Tuesday, the U.S. president let known his views and said he expected a tough time in any future negotiations with Iran no matter who was in the government.
"The difference between Ahmadinejad and Mousavi in terms of their actual policies may not be as great as has been advertised," he told CNBC.
"Either way we are going to be dealing with an Iranian regime that has historically been hostile to the United States," he added.
Several U.S. analysts have been cautioning for weeks against any giddy optimism over a Mousavi win and said he should not be seen as an easy sell in any negotiations over Iran's nuclear program, which the West suspects is aimed at building a bomb and Tehran says is peaceful.
The Obama administration has been grappling with how to approach the election turmoil in Iran, where the country's top legislative body said on Tuesday it was ready to recount votes amid the biggest street protests since the 1979 Islamic revolution.
Both Obama and other senior officials have expressed concern over a clampdown on protests but have also sought not to be seen as injecting the United States into the drama.
The State Department confirmed on Tuesday that it had contacted the social networking service Twitter to urge it to delay a planned upgrade that would have cut daytime service to Iranians who are disputing their election.
Twitter and Facebook have been used by many young people to coordinate protests over the election's outcome. Obama himself used these networking tools in his own campaign to spread his political message before being elected.
Twitter Inc said in a blog post it delayed a planned upgrade because of its role as an "important communication tool in Iran." The hourlong maintenance was put back to 5 p.m. EDT/2100 GMT, which corresponds to 1:30 a.m. on Wednesday in Iran.
The upgrade originally had been planned for Monday night in the United States, which would have cut daytime service in Iran on Tuesday.
The State Department declined to give details of its contact with Twitter, which has been used particularly by young urban Iranians who dispute Ahmadinejad's re-election.
"We highlighted to them that this was an important form of communication," said a State Department official of the conversation the department had with Twitter officials.
Any sign of U.S. involvement in the actions of Twitter or any other social networking service could be seized on by Iran as U.S. interference in the electoral process.
But State Department spokesman Ian Kelly strongly rejected that contacts to Twitter amounted to meddling in Iranian internal affairs.
(Additional reporting by Deborah Charles, David Alexander and Ross Colvin; Editing by Will Dunham)
