The zoo said in a statement that 5-year-old Tatu was found hanging with a rope around his neck Friday morning in a sleeping room. Spokesman Michal Stastny said all attempts to revive Tatu failed.
He said there are no cameras in the room and it is not clear exactly what happened.
Mammals curator Pavel Brandl said Tatu likely unbraided one of the dozens ropes the gorillas use in their pavilion for climbing and put a strand around his neck before hanging himself.
"It was an accident," Brandl said. He said the ropes are checked on a regular basis every day.
Brandl said another gorilla, Kamba, appeared to be trying to help Tatu when zookeepers arrived but "it's hard to say what exactly she was doing."
Director Miroslav Bobek said the death was the most tragic event at the zoo since flooding in 2002 killed more than 100 animals.
The zoo still has six gorillas, and they are among the most popular animals there. Tens of thousands of people watched Tatu's birth online on May 5, 2007.