Jestice James is facing two counts each of murder and child abuse under circumstances or conditions likely to cause great bodily injury or death, along with allegations of child endangerment, according to the Los Angeles County District Attorney's Office.
Evidence indicates fentanyl was involved in the case, prosecutors said.
James' bail has been set at $4 million. She appeared in court in Van Nuys Tuesday, but her arraignment was pushed back until July 31.
The boys were identified by family members and the Los Angeles County Department of Medical Examiner as Josiah James and Jestine James, also known as Juju and Jojo.
Family members spoke with Eyewitness News on Tuesday, saying they're hoping raise awareness on the dangers of fentanyl.
"Anyone who has a family member, a friend, an associate who is indulging in that particular drug to know that it is fatal drug," said the boy's godmother Regina Holmes. "We lost Juju and Jojo."
The boys celebrated their third birthday on July 9, just a few days before their deaths.
"They still had a long life to live that we hoped and wished to be able to see, but unfortunately, they were taken away too soon and way too young," said the boys' cousin Precios Padilla.
More cases involving children and fentanyl
According to Los Angeles County Deputy District Attorney Jonathan Hatami said there are currently five cases being investigating that involve children and fentanyl.
"I have five cases that I'm looking at - this is one of the five - so I have four additional cases, most of them are in and around Antelope Valley because I handle a lot of cases from the Antelope Valley that are dealing with children who have passed away, and fentanyl is involved in those cases."
He said he received those cases in the last six months.
Investigation continues
The medical examiner's investigation into the boys' official cause of death is ongoing.
Police and paramedics responded about 11:20 a.m. Thursday to a home in the 20000 block of Sherman Way, near Winnetka Avenue, where Jestice James found the boys "unresponsive," according to the Los Angeles Police Department.
The boys were rushed to a hospital, where Josiah was pronounced dead early Thursday afternoon and Jestine was pronounced dead Saturday, according to the DA's office.
"Preliminary investigation revealed that the children had ingested, or been exposed to, an unknown substance," according to an LAPD statement released Friday. "The mother and other residents of the home were transported to the LAPD Topanga Community Police Station for questioning."
Mother arrested after 3-year-old son dies, twin brother critical: LAPD
The boys' mother was arrested Thursday night by the LAPD's Juvenile Division/Abused Child Unit and has remained in custody since then, according to jail records.
Police said the other residents of the home are not being investigated any further.
James faces a potential life prison term if convicted as charged, according to prosecutors. Meanwhile, the family has created a GoFundMe to help with funeral expenses.
"Any help that anybody can do to add to that [so] we could give them a proper burial, it would be so greatly appreciated because the family has no money," said Holmes.
Anyone with information about the case is urged to contact LAPD Detective Ortiz at (818) 374-5415. During non-business hours or on weekends, calls should be directed to (877) LAPD-24-7 (877-527-3247). Anyone wishing to remain anonymous should call the L.A. Regional Crime Stoppers at (800) 222-TIPS (800-222-8477) or visit lacrimestoppers.org.
City News Service contributed to this report.