Maryland, US (BBN)-Barack Obama has condemned what he called "inexcusable political rhetoric" about Islam, an apparent reference to recent remarks by Republican presidential candidate Donald Trump.
In his first visit to a US mosque as president, Obama said anti-Muslim rhetoric had "no place in our country", reports BBC.
He praised Muslim-Americans as "some of the most respectful and patriotic Americans you'll ever meet".
Trump has called for Muslims to be banned from entering the US.
Obama was speaking at the Islamic Society of Baltimore mosque in Maryland.
He has visited mosques in other parts of the world on official trips abroad during his seven years as president.
The White House said the visit was intended as a defence of religious freedom and a statement against bigotry.
"The first thing I want to say is two words that Muslim-Americans don't hear often enough, and that is: thank you," Obama said at the start of his speech.
"Thank you for serving your community, thank you for lifting up the lives of your neighbours, and for helping keep us strong and united as one American family."
The president said he recognised that Muslim-Americans were being "targeted and blamed for the acts of a few".
"Most Americans don't know of don't know they know a Muslim person," he said.
"Many only hear about Muslims and Islam from the news after an act of terror, or in a distorted media portrayal on TV or in a film.
"Since 9/11, but more recently since the attacks in Paris and San Bernardino, you have seen too often people conflating the horrific acts of terrorism with the beliefs of an entire faith."
Advocacy group Council on American-Islamic Relations (CAIR) says it has tracked a growing number of attacks on mosques and Muslims since the Paris and San Bernardino attacks.
A report by the group warned that "levels of anti-Muslim sentiment follow trends in domestic US politics", highlighting Trump's call for a ban on Muslims entering the country.
Ibrahim Hooper from CAIR said: "I don't think there's ever been this level of fear and apprehension in the Muslim-American community.
"For some time, we've been asking for pushback. Perhaps this will start a trend."
Obama is in his final year as president.
A week ago, he became the first sitting president to speak at the Israeli embassy, where he warned of growing anti-Semitism.
Akbar Ahmed, an Islamic studies specialist at American University, said Obama had left it "literally to the last" to visit a US mosque, but he added: "Better late than never."
In 2010 the White House blamed a "misinformation campaign" for a growing belief that Obama was a Muslim.
Over the course of his presidency, some people have said he is a Muslim pretending to be a Christian.
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