The four bodies were found Nov. 11 in and around two shallow graves in the desert in Victorville, Calif., by a passing motorcyclist.
Officials were able to confirm the identities of Joseph and Summer McStay Nov. 15 through dental records, but DNA testing had to be done on the two smaller bodies in order to confirm their identities.
The California Department of Justice DNA Lab said Friday the bodies were that of Gianni, 4, and Joseph, 3, NBC News reported.
The family went missing Feb. 4, 2010, and their car was found in a parking lot at the San Ysidro border crossing.
Surveillance video from Feb. 8, 2010, showed a family seeming to match the McStays' description entering Mexico on their own. The alleged border crossing led to some speculation that the family was secretly involved in Mexican drug cartels, but the San Bernadino County Sheriffs Department said there was no evidence confirming that rumor.