Authorities in the United States said James Jordan, 57, whose body was found floating in a creek in South Carolina, died of a gunshot wound to the chest from a .38 calibre weapon.
Michael Jordan, whose huge success with the Chicago Bulls has earned him fans worldwide but whose image has been marred by gambling scandals, made no immediate public statement.
His father's decomposed body was found in a river 11 days ago, but officials said it took some time to identify using dental records. Nine days ago, Mr Jordan's luxury red Lexus car was found about 50 miles away, near Fayetteville, in the neighbouring state of North Carolina. It had been stripped of its fittings and vandalised.
Concern about Mr Jordan's whereabouts had been growing since the discovery of his car. He had last been seen attending a funeral of a friend in Burgaw, 60 miles from Fayetteville, on 22 July. His wife has told authorities that she last spoke to him four days later. The authorities said they had no suspects, nor had they determined any motive for the killing - but the FBI said a kidnapping investigation had begun.
The death of his father is another blow to Michael Jordan, whose once-flawless career has recently been marred by off-the-court troubles, mostly related to gambling. His huge popularity - polls among youngsters in Britain, Europe and even China have placed him at or near the top - has earned him millions. He led the Chicago Bulls to three consecutive victories at the National Basketball Association finals, and was a member of the 'dream team', the 1992 US Olympic basketball team.
But a cloud descended this summer when a San Diego businessman and former friend published a book alleging that the basketball star refused to pay a dollars 1.2m ( pounds 821,000) gambling debt run up on the golf course in 1991. Much of the debt has been settled, although his accuser recently claimed Jordan still owes him dollars 100,000.
Jordan began this season with a reprimand from the National Basketball Association for betting on golf games. And last year he was called to testify in a court case after a dollars 57,000 cheque from his account was found in the possession of an alleged drug dealer and money launderer. Jordan admitted that he had lied when he originally said the money was a personal loan. In reality, it was payment for losses incurred during a poker weekend.