Ricardo Santiago, 34, of Millville, was charged after surrendering on Tuesday night, police in Vineland, New Jersey said. He is being held on $1 million cash bail.
Also Tuesday night, the bodies of 34-year-old Neidy Ramirez and her daughter, Genesis, were recovered.
Police say Santiago led officers to the bodies, which were in a rural area of west Cumberland County. Police did not give a specific location.
While the motive remains under investigation, police appear to have some indication as to what happened.
"They were co-parents and it appears there was some sort of dispute," said Lt. Matthew Finley of Vineland City police.
Investigators did not say if there were any obvious signs of trauma. The New Jersey State Police Crime Scene Unit was at the location.
Police said the family of the victims, including baby Genesis' biological father, have been notified.
Ramirez had two other children, a 5-year-old and an 8-year-old. Police said Santiago is the father of the 5-year-old. Those children are now with family members.
Vineland police say Ramirez and Genesis spent time with family on Thanksgiving, and they were last seen at a laundromat on Friday.
On Saturday, a co-worker found Ramirez's abandoned 2005 Chevy Trailblazer on northbound Route 55 near milepost 45.3.
When Ramirez didn't show up for work Monday morning, the friend informed others. The family went to Route 55, saw the vehicle, and immediately called police.
Detectives say Santiago has been cooperative. He is scheduled to be arraigned at 1:30 p.m. Thursday.
As the investigation continues, Vineland police ask anyone with information is asked to call them at (856) 691-4111 x4180 or the Cumberland County Prosecutor's Office at (856) 453-0486.