The meeting in the Cuban capital's Palace of the Revolution is only the third formal encounter between Obama and the brother of Fidel Castro, who handed over the presidency in 2008.
At stake is the historic shift to end the Cold War conflict, which has seen Washington try to bring Cuba to its knees through an economic embargo, while Havana, a close Soviet ally, became enemy territory.
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As Air Force One landed in Havana, Obama cheerfully began the landmark trip by tweeting in local slang: "Que bola Cuba?" -- or "What's up?"
Later he noted that the last US president to come, Calvin Coolidge in 1928, needed three days to make the trip by train and navy ship.
"This is a historic visit," he remarked to staff at the freshly reopened US embassy in Havana.
The trip has been touted mostly for its huge symbolic value, and comes more than a year after Obama and Castro surprised the world in December 2014 by announcing that their countries would begin normalising relations.
"The presence of a US president on the island for the first time since the 1959 revolution marks a transcendental change in relations between the US and Cuba," said Michael Shifter, head of the Inter-American Dialogue thinktank.
But some tough issues are up for discussion. Although the embargo can only be lifted by Congress, where Republicans are far less keen on rapprochement, the Obama administration is chipping away at the edges of the sanctions.
For example, a trickle of US visitors over recent years is soon expected to turn into a flood with the lifting of an onerous requirement that they go to Cuba as part of pre-approved groups.
But while pushing for an easing of the decades-long sanctions regime, the White House continues to press for greater human rights in a country where the Communist Party maintains its grip on every key institution and little dissent is tolerated.
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