On April 1, 1865, he was found by his son, William Henry Milton. His death from a fatal gunshot wound to the head was reported as an accident by his family, church, and the "West Florida News". "The New York Times" assumed Governor Milton’s death to be suicide at the prospect of Union victory and Republican government. The president of the Florida Senate, Abraham K. Allison, was sworn in as governor of Florida later that day. Asserting that the governor has recently stated to the legislature that he did not want to live under the prospective oppression of a lost cause, the New York Times writer drew his own conclusions. The article is polemic in tone. Milton was found by his son at the Milton plantation, Sylvania, in Jackson County, Florida. He had suffered a fatal wound to his head. The West Florida News reported the sudden death of Florida’s fifth governor as a hunting accident. Governor John Milton was buried in the Episcopal cemetery at Marianna, Florida, near his home, Sylvania. Several recent works have investigated the event and discovered that the death was probably from an accident as Milton prepared for hunting.