The discovery was made in the 2500 block of Hesperian Street.
"We had somebody bring over a tractor and they just put it underneath and they lifted it and a skull just fell over," said the homeowner, who did not want to be identified.
Police said the homeowners were not suspected of wrongdoing. The homeowner said she bought the house from her next door neighbor after it was nearly destroyed by a fire in 2006.
Investigators discovered more remains on the property.
"At this point, because the bones are partially still covered, we're all backing off waiting until tomorrow morning until an anthropologist can come here and go through the tedious details of unearthing the remainder of the bones," said Anthony Bertagna of the Santa Ana Police Department.
The home was recently rebuilt and her adult children took up residence.
Neighborhood residents describe the former owner as a recluse.
"I just used to see the man come out of the house, very strange," said neighbor Tina Gutierrez. "The house was a mess. A lot of overgrown plants in the front yard."
According to the homeowner, the man, who had lived in the house for many years, once said something suspicious.
"He told my husband that he had a dog and puppies buried in the back, that when we were ready to let him know, because he wanted to come and get the dog for his sister," the homeowner said.