Boise police said zoo security called about 4:30 a.m. to report the male Patas monkey was found mortally injured near a perimeter fence and two men were spotted fleeing the area, Boise Weekly reported.
The Idaho Statesman said police recovered blood evidence from the scene and were having it tested to determine if it came from the monkey or one of the break-in suspects.
The Statesman said a zoo security guard reported seeing one person outside the fence near the primate exhibit and a second man inside who ran off.
Zoo Director Steve Burns said police arrived and during the search for the suspects they heard a groaning sound.
"We didn't know what it was, whether it was an animal or a human," said Burns, adding it turned out to be the injured monkey.
Burns said the monkey, which stood about 2 1/2 feet tall and weighed 35 pounds, died a short time later and a necropsy showed it died of blunt force trauma to its head and neck.
A second Patas monkey that shared the same cage was not harmed.
The fatal attack shocked the zoo staff, Burns said.
"One of the staffers said it feels like someone broke into their house and harmed one of their children," he said.
"Visitors also get attached to favorite animals. And the monkeys are always among the favorites. It's going to be hard to explain to kids that there are people in the world who would do something like this."
Patas monkeys are not endangered in the wild but only 52 live in U.S. zoos. Zoo Boise has had Patas monkeys for three years.