The father of a 3-month-old baby found dead inside a Bronx apartment last night is a formerly homeless veteran who struggled with mental illness and had lost custody of another baby in the past.

Police are investigating after they say the infant of Mark Ruane was found dead in his family’s Ogden Ave. home in Highbridge.

His mother found him and called 911 around 11:30 p.m. and the unresponsive child was rushed to Bronx Lebanon Hospital and pronounced dead, police said.

The Administration for Children’s Services took dad Mark Lodger Ruane’s daughter Emerald shortly after she was born in 2015, according to a lawsuit he and the mother filed against the city last year.

Ruane and the tot’s mom Alexondra Ambrocini claimed in court document that two social workers had falsified a case against them, accusing Ambrocini of testing positive for cocaine before the birth.

The case is still ongoing — just last month, Ruane filed a letter requesting a new court date, saying he couple had split up and that he was busy moving out of their apartment, court documents show.

Five years ago, Ruane didn’t have a home at all. The army was profiled in a 2012 story, living and panhandling on West 32nd Street as he struggled to get help from Veterans Affairs for his bipolar disorder.

The Medical Examiner’s office will determine the official cause of baby Mark’s death, officials said.