Police said they found Kayleigh dead in her bed Saturday afternoon after being asked to check on her welfare in a unit in the Royal Garden apartments on Wilkins Avenue.
Kayleigh had suffered blunt force trauma and appeared to have been sexually assaulted, police said.
According to police, the girl's mother, Sara Krueger, 23, and her boyfriend, Ryan Scott Warner, 26, were seen leaving Krueger's house, carrying luggage, around 10 a.m. Saturday.
They were found around 11 a.m. Sunday with the help of an anonymous citizen, police said. BART police officers detained the couple at the El Cerrito Del Norte BART station until Napa Police could pick them up.