Mr Obama urged the release of Cuba's political prisoners
The US president has urged Cuba to respect the rights of its people, condemning it for treating its citizens with a "clenched fist".
Barack Obama said those who dared to voice the aspirations of their fellow Cubans were punished for their bravery.
Cuban dissident Orlando Zapata Tamayo died after starving himself to death in protest in February.
Urging the country to release its political prisoners, Mr Obama described such events as "deeply disturbing".
"I remain committed to supporting the simple desire of the Cuban people to freely determine their future and to enjoy the rights and freedoms that define the Americas," he said in a written statement.
He also urged "the immediate, unconditional release of all political prisoners in Cuba and for the respect for the basic rights of the Cuban people".
Zapata Tamayo's death, he said, was an illustration of how the Cuban authorities: "instead of embracing an opportunity to enter a new era... continue to respond to the aspirations of the Cuban people with a clenched fist".
Analysts have described Mr Obama's words as some of the toughest from the US administration since he took office 14 months ago.
Last month he sent a high-ranking envoy to Cuba to hold fresh talks on migration issues.
A week ago, Cuban police detained the wives and mothers of political dissidents as they took part in a demonstration in solidarity with Zapata Tamayo's mother, in the capital, Havana.
The women - known as the Ladies in White - were later released. They had been demanding the release of some 50 government critics held since mass arrests in 2003.
The case of Zapata, the first Cuban activist to starve himself to death in protest in nearly 40 years, drew international condemnation.
The Cuban government describes the dissidents as common criminals paid by the US to destabilise the country.