Tsuyoshi, a four-year-old "male" polar bear, and his 11-year-old female partner, Kurumi, have been living together since June at the Kushiro Municipal Zoo in Hokkaido, northern Japan.
But much to the frustration and puzzlement of zookeepers, the bear couple, on a breeding mission, showed no signs of chemistry, and Tsuyoshi has never gone into rut even during "his" mating period.
"Observing his behaviors, we got suspicious as to whether Tsuyoshi was really a male," the zoo said in a statement.
The zoo put Tsuyoshi under an anesthetic earlier in the month for a gender checkup, and learned he was a she.
"I have mixed feelings," Yoshio Yamaguchi, head of the zoo.
Tsuyoshi is very popular at the zoo, and Kyodo News agency said the zoo would not change his name to a female name. Tsuyoshi is a very common Japanese name for boys.
Experts say when polar bears are young, it is difficult to determine their gender as their long hair covers reproductive organs.
The zoo said it had determined Tsuyoshi was a male three months after his birth.