Deputies said they confirmed the deaths through their investigation, but the bodies have not yet been found. They will continue to search throughout the night.
No one has been charged yet.
The mother, Yessenia Suarez, 28, her 8-year-old son, Michael Otto, and 9-year-old daughter, Thalia Otto, were not at their home on Covent Gardens Place in Deltona when deputies arrived for a well-being check.
Related Story: Voulsia mom & 2 kids missing
According to deputies, a family member of Suarez called and asked for the well-being check Wednesday morning.
A family member said her husband, Luis Toledo, had shown up at her place of work in Lake Mary on Tuesday and hit her, and that Suarez was afraid of Toledo.
Authorities obtained a search warrant Wednesday night and were taking photographs and video inside the home in hopes of uncovering evidence that could explain their disappearance.
Shortly after deputies arrived at the home Wednesday, they said Toledo showed up.
"A few minutes after being on scene, Mr. Toledo came on scene and started talking to deputies and causing a bit of a disturbance," said Volusia County Sheriff's Office spokesman Brandon Haught. "We found out he had charges pending on him from Lake Mary, and we asked Lake Mary if they would like to come arrest him, and they did so."
Suarez has two vehicles registered to her name. One was found in the driveway of her home, while the other was found in the parking lot of a Publix store in Lake Mary.
Toledo was arrested on a domestic violence charge and taken to the Volusia County Jail, where investigators said they were questioning him about his wife's whereabouts. He was expected to face a judge Thursday afternoon, but his appearance was delayed because officials said he is starting to cooperate.
Toledo has an extensive criminal history, including several counts of aggravated assault, aggravated battery and one count of shooting into an occupied dwelling between 1997 and 1999. However, those charges were dropped.
He served a year in prison for a burglary in Orange County.
In 2000, he was charged with attempted second-degree murder and kidnapping in Orange County, but the case was dismissed before going to trial.
In June 2012, a woman requested a temporary injunction against him, claiming he sent her a series of text messages threatening to hurt her and take her children.
The Florida Department of Law Enforcement officially issued a missing child alert for the two children on Thursday morning.
Anyone with information is asked to call the Volusia County Sheriff's Office at 386-254-1535.
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