The charges were announced even as homicide detectives continue to search a Victorville landfill for the body of 6-year-old Duke Flores, who was reported missing from Apple Valley last week, according to the San Bernardino County Sheriff's Department.
Detectives believe the boy's body was placed in a dumpster.
"Detectives are now working with personnel at the landfill in hopes of recovering his body," the department said in a statement.
Flores' mother and aunt, Jackee Contreras and Jennifer Rachel Contreras, were arrested and booked on suspicion of his murder Saturday.
On Monday, the San Bernardino County District Attorney's Office announced it had filed a single count of murder against each of the sisters. Their arraignment is expected Tuesday in Victorville Superior Court.
MORE: Mother, aunt arrested for murder of missing 6-year-old boy, authorities say
The 29-year-old twin sisters were each being held without bail.
The investigation into the missing boy with autism began about 10 p.m. Thursday when Flores' grandmother requested a welfare check on him, authorities said. Deputies responded to a home in the 22000 block of Cherokee Avenue, where the boy's mother said he had not been seen in over a week.
Jackee Contreras was immediately taken in custody for alleged child neglect due to her delay in reporting her son missing, authorities said. Deputies conducted a search of the area that proved fruitless.
Jackee and Jennifer Contreras live together with two other children and Flores' father.
Investigators have not said exactly what led them to believe Duke was killed.
The investigation is ongoing.