Zoo security spotted the men in a secured parking lot at the zoo at about 11:40 a.m. Sunday. The intruders had jumped over a fence in the back of the zoo, police spokesman Officer Albie Esparza said.
Police responded and arrested the men on suspicion of trespassing. One, Augustus Standingrock, 20, of Cheney, Wash., was cited and released, while the other two were booked into jail because they did not have identification, Esparza said.
Those men were later identified as Sean Walsh, 18, and Kenneth Hardy, 19, both transients from San Francisco, he said.
Esparza said the case is not believed to be related to the theft of Banana-Sam, a 17-year-old squirrel monkey who was reported missing on Dec. 30.
In that case, vandals had cut into a perimeter gate, climbed atop a roof sheltering five primate exhibits and cut two holes in the mesh of the squirrel monkey exhibit.
Banana-Sam was returned the next day by a man who said he had spotted the monkey in some bushes in Stern Grove and was able to coax the animal into his backpack.
A $5,000 reward that was offered in the case is being withheld until police complete their investigation into the circumstances of Banana-Sam's disappearance and return.
Zoo spokeswoman Lora LaMarca said she can not recall the last time someone was arrested for trespassing at the zoo.
"It doesn't happen that often," LaMarca said. "It's not a common occurrence at all."
She said the zoo has security on duty 24 hours a day, which was beefed up after the monkey's disappearance.