The Alameda County Coroner's Bureau classified her death as a homicide after finding multiple gunshot wounds on her body.
WATCH VIDEO: Body of missing San Jose woman Stacey Aguilar found
She disappeared last week after leaving a party on Silva Avenue near Jackson Street in Hayward.
Residents said she left with her boyfriend and unharmed.
On Monday, Hayward police said Aguilar's body was found at noon on Saturday in a rural area off Morrison Canyon Road in Fremont. "We do have a person of interest in custody, we cannot release the name of the person until charges are actually brought with the district attorney," Hayward Police Department Chief Diane Urban said.
Neighbors told ABC7 News they called police nine times because of a rowdy house party.
Aguilar's mother who lives in Mexico, told ABC7 News by phone she was suspicious of Aguilar's boyfriend.
Urban said police arrested him, but for a different charge. "The boyfriend was arrested for domestic violence, and he is one of the persons who was questioned, and that's all I can provide to you at this point," she said.
Police said he was taken into custody the day Aguilar was reported missing and said the alleged domestic violence was against Aguilar, but they would not say he is a person of interest in this case.
The Alameda County Coroner has completed an autopsy, but cannot release a cause of death because of the Hayward police department's ongoing murder investigation.
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WATCH VIDEO: Hayward police investigate missing person case as homicide