The estrangement between the US and Cuba started in 1959 when Cuba's revolution overthrew a pro-American government. Guevara is a famous figure of the revolution.
Obama was also photographed in front of a mural of Camilo Cienfuegos, another Cuban revolutionary.
Check out photos of the moment and the Twitter backlash:
Obama poses in front of Che mural
President Obama was photographed in front of a giant Che Guevara mural during his historic visit to Cuba
A vintage car drives past the Interior Ministry building with the image of legendary guerrilla leader Ernesto 'Che' Guevara at Havana's Revolution square in Havana, Cuba on March 19, 2016. Political and economic reforms in Cuba will be a no-go area during talks between Cuban leader Raul Castro and US President Barack Obama, the foreign minister said in Havana Thursday. A vintage car is parked in front of a building with an image of former Cuban President Fidel Castro at Havana's Revolution square on March 19, 2016. On Sunday, Obama will become the first sitting US president to visit Cuba since 1928, capping his historic policy of ending a bitter standoff that has endured since Fidel Castro's overthrow of the US-backed government of Fulgencio Batista in 1959. AFP PHOTO/ Yuri CORTEZ / AFP / YURI CORTEZ (Photo credit should read YURI CORTEZ/AFP/Getty Images)
Univision suggests a Cuban government plot to plant Obama in front of the Che mural. https://t.co/uSOHfEXjH2
Good to know Obama's priorities. Ol, Che Guevara. https://t.co/SpWKygwaUC
Obama proudly poses w/ Marxist murderer Che Guevara. Freedom advocates everywhere mournfully ask: Where is America? https://t.co/H8sTqB8tMk
So, Obama couldn't make it to Chris Kyle's memorial service, but he will stand at attention for Che Guevara. https://t.co/SKPHdQRMCJ
For those wondering about Obama's photo with the mural of Che, here's Che on blacks in "The Motorcycle Diaries." https://t.co/MucoE2BkNO
Right now Jay Carney is having a glossy print of that Obama-Che photo framed and put on his kitchen wall.
Sadly, Obama's photo-op in front of a Che Guevara mural is only offensive to those who actually know history. In other words, not many.
May be the picture of the day: Obama and Che. #ObamainCuba https://t.co/FumauXqRcR