The theft was discovered as keepers checked the monkey cages on their morning rounds and noticed two holes in the squirrel monkey exhibit.
Curator of Primates Corinne MacDonald says her team quickly did a head count and discovered that a 17-year-old squirrel monkey named Banana Sam was missing.
"Well the one hole is fairly small and it's right by where their nest box is that they sleep in at night and the other panel is fairly large, a small person could certainly go in," MacDonald said.
MacDonald suspects there were at least two people who cut the chain on a perimeter fence, climbed a staircase to the backside of the monkey exhibit and grabbed Banana Sam.
"It is really tragic that this animal might be by himself; it's very important that we get him back and we get him back with his family group," MacDonald said.
MacDonald says Banana Sam's diet is very specialized. Banana Sam is also a grandfather; squirrel monkeys live to be around 20, so at 17 he is one of the oldest monkeys in the exhibit.
Banana Sam is the latest in a string of squirrel monkeys stolen from other parks and zoos.
"Unfortunately these particular primates are popular in the primate pet trade," MacDonald said.
It is illegal to possess one as a pet in California, but that's not true for all states and prices range from a few hundred to several thousand dollars for handfed babies. But wild ones like Banana Sam do not make good pets.
The zoo is hoping whoever took the monkey will reconsider. The last time an animal was stolen from the zoo it was found a couple of days later.
In the meantime, the zoo will step up security and Banana Sam does have a microchip implant so he can be identified if he turns up.
At the zoo Friday, reaction to the theft was universal.
"That's kind of shocking," one zoo visitor said.
"I just think it's terrible," said another.
Elsewhere in San Francisco, there seemed to be a bit of a sense of humor related to Banana Sam's disappearance. Someone created a parody Twitter account and was tweeting Banana Sam's imagined adventures through the city. But Anthony Brown (@anthonybrown), a penguin keeper at the zoo, was not amused by the @SF_BananaSam account, tweeting "Let's start doing parody twitter accounts for kidnapped children! That would be hilarious. #vent"
The zoo is offering a $1,000 reward for Banana Sam's safe return.
This story is from our sister station, KGTO-TV in San Francisco.