A question mark has hung over which of the zoo's tribe of chimps courted Beni's mother Sally.
But a paternity test from hair samples has now revealed that chimpanzee Sammy is Beni's dad.
Keeper Cassandra Butler said she was not surprised by the results because Beni's mother was Sammy's favourite female.
"He [Sammy] is not the alpha male, I guess you'd call him a lover, not a fighter," she said.
Beni celebrates his first birthday tomorrow, but Ms Butler said he was still very much a baby.
He has integrated well with the group and made many friends, including the alpha male, she said.
Chimpanzees are endangered and Wellington Zoo's breeding programme is carefully managed to ensure offspring like Beni are healthy and genetically diverse.
Beni's birthday party is being held at the zoo on Labour Day.
