In an announcement issued Thursday, the zoo said Merlin had been sick and, after a "decline in his medical condition," the decision was made to put him down.
It was a long and eventful life for the lion.
He was born at the Johannesburg Zoo in South Africa in July 1991 and arrived in Philadelphia in July 1993 with three female lions.
Merlin and his pride were briefly relocated to the Columbus Zoo in 2004, but returned to Philadelphia for the opening of First Niagara Big Cat Falls in 2006.
Merlin fathered 11 cubs during his lifetime.
"During his many years in Philadelphia, Merlin remained one of the Zoo's most popular animals, often delighting visitors with his healthy roar," said zoo spokesperson Dana Lombardo.
The three female lions that came to Philadelphia with Merlin are still living at the zoo.