The girl's father, Brett Anderson, made an emotional plea on Tuesday for his missing daughter, Hannah. Anderson did not make reference to his 8-year-old son Ethan, who was also missing.
Anderson said he's been robbed of everything. He pleaded to the suspect, 40-year-old James DiMaggio, asking him to surrender.
"I'm begging you to let my daughter go. You've taken everything else," he said. "Hannah, we all love you very much. If you have a chance, you take it. You run. You'll be found."
Investigators believe DiMaggio, 40, murdered the girl's mother, Christina Anderson, at a house in Boulevard, east of San Diego, and then set fire to the home late Sunday night. A young boy's body was also discovered in the rubble.
Officials say it will take two or three days for DNA testing to determine if the charred body is in fact that of 8-year-old Ethan Anderson.
"It is a possibility that it's Ethan," said Lt. Glenn Gianntonio with the San Diego County Sheriff's Department. "Right now we just don't know."
Angelina Amati, a good friend of the family, says DiMaggio was a platonic friend who wanted more.
"I honestly believe that Jim has snapped and couldn't handle the infatuation that he had with Hannah," said Amati.
Investigators believe DiMaggio is driving a blue 2013 four-door Nissan Versa with the California license plate 6WCU986.
"We received some information that either Texas or Canada may have been the destination he was heading to. Realistically, we don't know where they're going," said Gianntonio.
This case led to the first-ever use of the cellphone Amber Alert system Monday night, which startled many people.
You're automatically opted into the cellphone system, but you can opt out. On an iPhone, you just go to settings, notifications, and then turn off "Amber Alert." But emergency officials urge you not to turn it off because they say it could save lives.
"Somebody out there knows something," said Bob Hover from the National Center for Missing and Exploited Children, who is in charge of sending the Amber Alerts. "The more eyes and ears searching for a child in a critically dangerous situation are way better and far outweigh the eyes and ears of just a couple."
Anyone with information was asked to call the San Diego Sheriff's Department at (858) 565-5200.
The Associated Press contributed to this report.