As his guest became the first leader of his country in almost 50 years to visit the White House, Obama praised Myanmar's journey away from brutal junta rule and promised Washington would offer more political and economic support.
Seated with Thein Sein in the Oval Office, Obama said previously tortured US-Myanmar relations had eased because of "the leadership that President Sein has shown in moving Myanmar down a path of both political and economic reform."
The US president said that Thein Sein had made "genuine efforts" to solve the intricate ethnic wars that have long torn at Myanmar's unity, but spoke out on the plight of Rohingya Muslim minority.
He expressed "deep concern about communal violence that has been directed against Muslim communities inside Myanmar.
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"The displacement of people, the violence directed towards them needs to stop," Obama said.
"For democracy to flourish in our country, we will have to move forward, and we will have to undertake political reforms and economic reforms," he said.
The visit went ahead even though critics say Obama's invitation was premature and takes pressure off Myanmar to address abuses such as recent anti-Muslim violence to which security forces allegedly turned a blind eye.
Thein Sein, who took office as a nominal civilian in 2011, surprised even cynics by freeing hundreds of political prisoners, easing censorship and letting long-detained opposition icon Aung San Suu Kyi enter parliament.
In an interview with the Washington Post published today, Thein Sein would not take a position on whether the Nobel laureate would be allowed to stand -- saying the future direction of reform was up to parliament.
But he is also not budging on the constitution's allocation of 25 per cent of seats in parliament to the armed forces, saying that the military had preserved Myanmar's independence.