Its same-sex penguin couple, Harry and Pepper, has split -- over a female, according to CBS station KPIX-TV in the City by the Bay.
The two had been together for six years. They nested together and incubated an egg laid by another penguin.
Zookeepers say, earlier this year, a female penguin named Linda became friends with Harry, after Linda's longtime companion died. That didn't go over well with Pepper, and led to a violent confrontation between Pepper and Harry.
Zoo officials kept the three penguins separated until recently.
They say Harry and Linda are now a happy couple and have successfully nested this year.