Zookeepers said 20-year-old Buddy and 10-year-old Pedro formed a bond after arriving at the zoo in May to join the newly opened African penguin exhibit, the Toronto Star reported Monday.
"They do courtship and mating behaviors that females and males would do,'' one zookeeper said.
"It's a complicated issue, but they seem to be in a loving relationship of some sort,'' said Joe Torzsok, chair of the Toronto Zoo board.
Experts said there have been other examples of same-sex penguin mating at zoos in New York, Japan, Germany and Sea World Orlando in Florida.
However, officials said the relationship is destined to come to an end as zookeepers plan to pair them with females for breeding. Officials said African penguins are endangered and the move falls under the species survival plan agreed upon by zoos.