Two of four bodies found in shallow graves in the desert north of Victorville are those of Joseph and Summer McStay, but it remained unclear Friday if the other bodies were those of their two young sons. Courtesy FOXE FIVE News

POLICE confirmed bones found in the California desert this week belonged to the missing McStay family who disappeared from their home in February 2010.

Law enforcement officials announced on Thursday that skeletal remains found in Victorville had been identified as Joseph McStay, 42, and his wife Summer, 45, The Los Angeles Times reports.

Two other small bodies are believed to belong to the couple's sons, Gianni, 4, and Joseph Jr, 3. Further tests are being done to confirm their identities.

The quiet suburban family have not been seen since they left their Fallbrook home without a word of goodbye in February 2010.

But now the mystery of whether the McStays are still alive has been answered, authorities have launched a new investigation into the suspicious circumstances of their death.

San Bernardino County Sheriff John McMahon said the deaths have been ruled as homicides.

The cause of death will not be released because of an ongoing investigation.

One theory had been that the McStays had fled the United States for Mexico.

Officials reviewed surveillance footage from the border crossing which showed a family close to the McStay's description crossing the border to Mexico.

Surveillance footage at a border crossing featured a man holding the hand of a young boy followed by a woman holding the hand of another boy.

Sheriff McMahon said Friday the family may not have been the McStays.

The family's remains were discovered earlier this week when an offroad motorcylist discovered a pile of bones 50m from a dirt road and reported them to the sheriff's department.

Investigators excavated the site and made the grim discovery of two shallow graves containing the remains of four people.

Joseph's brother Mike notified the authorities a few days after the family went missing in 2010.

When police searched their house they found no sign of foul play. A carton of eggs sat on the counter, two bowls of popcorn on the futon and two dogs in the backyard, suggesting the family may have left in a hurry.

Their dogs had been left without food or water and the neighbours had been feeding them.

Since they vanished, the family had not used their mobile phones, credit cards or touched the $100,000 in their bank accounts.

"The bottom line," the lead investigator in the case, Troy Dugal, told The Los Angeles Times in 2011, "was that life was normal for the McStays up to February 4, and on that day they just vanished."

Someone had conducted online searches about Mexican border crossings on the family computer before they vanished.

Investigators discovered the family's car had been towed from the car park of a shopping mall in San Ysidro, an hour's drive from the family’s home and a short walk from a pedestrian crossing into Mexico.

Joseph's father Patrick was convinced the family had not fled to Mexico.

"My son didn't walk away," Patrick McStay said on Thursday. "They didn't walk into Mexico. They would never do that."

He said he suspected foul play early on. There have been suggestions the deaths could be related to a Mexican drug cartel.

Sheriff McMahon said it's too early to tell if there was cartel involvement. Despite the discovery of the bodies, too many questions remain unanswered for Patrick McStay.

"It's far from being done yet - far from being done," he said. "It won't be done until I find out what happened, and why, and who."