The zoo wants to split up the two African penguins, named Buddy and Pedro, to make them mate with females as the species is endangered.
Buddy, who is 21, has produced offspring with a female partner who later died, but Pedro, 10, hasn’t had any yet.
Tom Mason, a zookeeper at Toronto Zoo said that the penguins’ relationship was social, and probably not sexual, and that their bond had formed as part of a “bachelor flock” at another zoo.
But there has been a backlash from gay websites and bloggers, who have called the zoo “gay hating”.
Others have said it was an attempt to force the penguins into the “patriarchal sex trade”.
Blogger Bill on Youngnotions.com said Toronto Zoo was “interfering with true love”. He also encouraged allowing marriage between gay penguins.
The website Gawker called Canada “evil and homophobic” and said: “They probably wouldn’t have sex with a woman if they were the last penguins on earth anyway.”
Comic Jimmy Kimmel called their story “Brokeback Iceberg”.
The zoo says that once the penguins have mated, they will be allowed to rekindle their relationship.