Honoring a man whose writing is still read by young Cubans, Obama touched a wreath and signed a memorial book at the foot of a statue in the heart of Havana's government district.
The moment began with a band from the General Staff of the Revolutionary Armed Forces of Cuba playing the Star-Spangled Banner.
Images of the event were broadcast on Cuban television.
Marti was a leading figure in Cuba's battle for independence from Spain.
He also ties the United States and Cuba, having lived for years in exile in New York, where he championed independence through his journal "Patria" -- or homeland.
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Marti died in Cuba in 1895 in a battle against the Spanish.
Secretary of State John Kerry said the Obama visit was "a historic moment," adding that it was "pretty remarkable to hear the anthems here, side by side, in Havana with the president of the United States."
After signing the memorial book Obama walked across Revolution Square under the gaze of a mural of revolutionary icon Che Guevara to a meeting with Cuban President Raul Castro.