Florida cheerleader Anna Kepner’s 16-year-old stepbrother is an FBI “suspect” in her killing, according to court documents — as troubling allegations emerged about her blended family.

The revelation came from a messy custody dispute between Kepner’s stepmother, Shauntel Hudson, and her ex-husband — both of whom have filed legal briefs attempting control custody of the two minor children they share.

Chillingly, Shauntel accused her ex Thomas of domestic and physical abuse against their two youngest children — including the boy who is now being questioned by the FBI in the high school senior’s mysterious death, according to an emergency motion filed in court Monday and seen by The Post.

She said Thomas is the subject of an active Florida Department of Children and Families investigation, according to the docs.

The stepbrother, who was identified as “TH” in documents, remains in the care of one of his mother’s relatives as the investigation into Kepner’s death on board a Carnival cruise ship on Nov. 7 continues, according to the legal filings in a Brevard County family court.

Thomas fired back, accusing Shauntel of a “violent altercation” with the couple’s oldest son, who is an adult. The fight allegedly involved Shauntel and her new husband, Christopher Kepner — Anna’s father, according to court documents.

The allegations, which Shauntel disputes, came to light after she went to court to try to postpone a hearing scheduled for December to address custody issues with her former husband, from whom she divorced in 2023.

Thomas also blames his 16-year-old son’s legal trouble on his ex-wife’s decision to keep him away from his father, saying his “future has been put in jeopardy because of the choices made by” Shauntel.

Shauntel Hudson and two of her children set sail Nov. 2 on the Carnival Caribbean cruise that would end in tragedy, along with Christopher and Anna.

Anna was reportedly found dead in her room wrapped in a blanket and covered in life jackets at the tail end of the six-day cruise.

The ship returned to the Port of Miami the following day as scheduled.

Despite the apparent family strife, Anna’s memory was honored in a touching tribute published in the wake of her death.

She was remembered by her family as a “beauty” who “lived every day with her whole heart,” and who hoped to become a K9 police officer after joining the US Navy.

“She loved the sun, the water, boat days, island days, and beach days, anything that let her soak in the light she so easily radiated to others,” the family wrote in the obituary, in which they referred to the 18-year-old by her nickname, “Anna Banana.”

“She never had a filter, and that was part of her charm,” they heartbreakingly recalled. “She had a big, beautiful heart, often sending random ‘I love you’ messages or little gestures that made someone’s day,” the missive read.

The FBI’s Miami office, which is investigating the death because it took place in international waters, gave no further updates Wednesday.

No official cause and manner of death has been given by the Miami-Dade County Medical Examiner’s Office, which is handling the teen’s autopsy.

No charges have yet been filed in the case.