According to police, a security guard spotted two men Saturday wearing dark clothes outside the fence near the primate exhibit. Both fled, with one heading into the zoo's interior. Boise police used a thermal imager to search the 11-acre zoo but couldn't find him.
During the search, investigators heard a groan that at first was thought to be human. It turned out to be an injured Patas monkey barely moving near the perimeter fence.
The zoo's veterinarian was called, but the monkey died just before 6 a.m. as it was being examined. A necropsy later determined that blunt force trauma was the cause of death, police said.
Investigators hope a gray baseball cap with a distinctive skull design found near the site can help track down the suspects. Police are also analyzing blood found at the scene.
No other animals were hurt.
The Associated Press contributed to this report.