A mom of three was found dead in a Bronx homeless shelter where she was living with her kids, according to police and family.

Security personnel from the shelter discovered the naked body of Aneida Vidal, 45, lying face-up on the floor of the first-floor room of BronxWorks on E. 138st Street near Cypress Avenue in Mott Haven just before 8 a.m. Thursday, police sources said.

She was pronounced dead at the scene, police said.

Cops said an unidentified man was seen fleeing the room, but she had no obvious signs of trauma. The medical examiner is yet to determine her cause of death.

Vidal had been living at the shelter for two months with her seven-year-old twin sons and 13-year-old daughter, her father, Angel Vidal, told The Post.

“We don’t know what happened,” said an anguished Angel, 69. “We have a lot of questions and we are looking for answers.”

“She was a nice person and a very good mother,” he added.

The rear of the shelter was taped off as a crime scene Friday. The New York City Department of Homeless Services is investigating this case.

The medical examiner has