Heather Leavell-Keaton, who was extradited from Kentucky, is being held without bond, a sergeant at the jail said.
Over the weekend, search teams uncovered human remains in Alabama that police believe belong to one of the children. Search teams found the skeletal remains near a county road in Citronelle, about 30 miles north of Mobile, said Mobile Police Maj. Kara Rose.
Rose said investigators believe the remains are those of Natalie DeBlase, who would have turned 5 in late November. Skeletal remains found last Wednesday in the woods of rural Mississippi are believed to be those of her 3-year-old brother, Chase.
The children's father, John DeBlase, 27, is charged with two counts of felony murder and two counts of corpse abuse.
Police have said Leavell-Keaton, DeBlase's common-law wife, also is responsible in the killings. She has been charged with child abuse but not with the deaths.
Mobile County Assistant District Attorney Jo Beth Murphree said Friday that authorities would soon upgrade Leavell-Keaton's charges from child abuse to more serious aggravated child abuse counts. Leavell-Keaton also was to be charged with two counts of corpse abuse.
DeBlase's court-appointed attorney, Jim Sears, has said DeBlase maintains that he is innocent and that Leavell-Keaton killed the children. She has blamed DeBlase for the children's deaths.
Attorneys for DeBlase have said he will plead not guilty by reason of mental disease or defect. Sears said Friday that comments made by friends that called into question DeBlase's mental health are "certainly not without reason."
DeBlase had told police he dumped his daughter's body in the woods north of Mobile in March. He said he discarded the boy's body, dressed only in a diaper and stuffed into a plastic garbage bag, in Mississippi in June on or around Father's Day. Police say the children were killed separately, then immediately disposed of.
An investigation into their disappearance didn't start until late last month after Leavell-Keaton sought a protective order against DeBlase in Kentucky. She said in the Nov. 18 filing that DeBlase may have killed his children, and that she feared for her life because he was abusive. The couple had a child together this summer. That child is in state custody in Kentucky.
Meanwhile, arrest warrants in the case accuse Leavell-Keaton of abusing the boy and girl.
The documents accuse Leavell-Keaton of binding the girl's hands and feet with duct tape, putting a sock in her mouth and stuffing her in a suitcase in a closet for about 14 hours.
The warrants also accuse Leavell-Keaton of duct-taping the boy's hands to the side of his legs, strapping a broom handle to his back and shoving a sock in his mouth, then forcing him to stand in a corner all night while the adults went to bed.
The documents say the abuse happened sometime after March 1.