The owner of that home, 40-year-old James DiMaggio, is suspected of killing 44-year-old Christina Anderson and abducting one or both of her children.
Sheriff's investigators said that Anderson's body was found Sunday night and that she is a victim of a homicide. They did not say how she was killed.
In a burned garage was the body of a child whose identity and manner of death remain undetermined. A dog was also found dead inside the house.
Authorities wouldn't say whether the body may be one of Anderson's two children, 16-year-old Hannah and 8-year-old Ethan. An Amber Alert was issued for the children.
Authorities say DiMaggio was in a close platonic relationship with Anderson. Dimaggio is believed to be driving a blue 2013 four-door Nissan Versa with the California license plate 6WCU986.
Anyone with information was asked to call the San Diego Sheriff's Department at (858) 565-5200.
The Associated Press contributed to this report.