Bush, the former Florida governor, credited South Carolina Republican Gov. Nikki Haley's decision to endorse removing the flag via Twitter:
In recent days, Bush had spoken directly with Haley on the issue, according to aides, who declined to share details of the conversation.
In early February 2001, Jeb Bush quietly ordered the removal from State Capitol grounds of "The Stainless Banner," a mostly white flag that featured the Confederate battle flag design in the top left corner.
The flag flew outside the west entrance of the Capitol in Tallahassee with three other flags memorializing the history of the Sunshine State. Bush had decided to remove the flags in December 2000 -- in the wake of a bitterly contested presidential campaign that featured both a primary season debate about the Confederate flag, and the protracted recount that resulted in his brother's election as president. Two months later, they were gone.
Before his decision, Bush had already telegraphed his opinions on the flag. In Jan. 2000, as national organizations began pressuring Southern states to remove the Confederate flag from public spaces and public property, a resident named Suzi Harper e-mailed: "What is your thoughts on this confederate flag issue?"
Bush responded: "I am happy that we don't have a confederate flag."
The flags came down quietly on a Saturday morning, and the decision went unnoticed for another eight days, until news reports spread the word. Within hours, Bush -- an avid e-mailer who urged Florida residents to write to him directly -- started receiving often-heated criticism in his inbox.
"You are not from the South," wrote Carole Shelton. "You have no right to impose your northern prejudices and misconceptions on the people of Florida and to snub your nose at its history. I demand that the flags be returned to their original place, around the fountain or in front of the old capitol."
"Carole," Bush wrote, "soon you will be able to see the flags in the Florida History musuem [sic]. They will be respectfully displayed."
He added: "PS I am a Floridian born and raised in Texas."
Jim Jenkins of Madison, Fla. angrily wrote to tell Bush: "You are a YANKEE trying to run a Southern State, you just don't get it do you??"
"Sir, I voted for you, but NEVER again," he added. "I know you will never read my e-mail as you''ll have one of your flunkies respond."
Bush replied: "Mr. Jenkins, I am reading your email and I don't have flunkies around me. You will be able to see the flags that flew over Florida in the Museum of Florida History proudly displayed."
Records suggest Jenkins never replied to Bush.
In a separate message, Wesley H. Frank told the governor: "I am disappointed in your feelings toward this state, your only here to get elected to the next higher political job, you only are worried about your image not Florida, her people, nor her proud history."
"I agree with you that the flags should be displayed as history," Bush wrote back. "That is why since there is a fountain project commencing where the flagpoles once were, they will be respectfully displayed in the Museum of Florida History."
Bush's decision to remove the flag came more than a year after he declined to issue a proclamation recognizing Confederate History Month -- an honor many of his predecessors had issued with regularity, because the month was used as a time to teach schoolchildren about the state's history.
Recognizing that the month had been advocated for educational purposes, Bush initially proposed signing a proclamation declaring "Civil War history." But the proposal was rejected by Confederate heritage groups, so he backed off and never signed a heritage declaration over his eight years as governor.
For years, his inbox was flooded with messages blasting his decision.
"I understand that it is a tourist state," wrote Jane Knowell. "But that doesn't alter [sic] the fact that it is still a southern state. I feel that in denying to designate April as confederate history month, you are telling the people of Florida that the only ones who matter to you are the ones who have moved here from up north."
Bush replied: "People of all origins matter to me. I have a great respect for our Southern Heritage and the heritage of those who came from other places as well."
An Orlando man named Mark Hopper also wrote to Bush, asking "I appeal to you to recognize this day. Many a brave man died doing not what he wanted, but what he was told to do by his state for the cause."
"I was prepared to recognize the day but using language that was not offensive and was respectful of the organization," Bush told him. "That effort was rejected. Rest assured that I am appreciative of your contribution to our state."
In another message, Bush wrote that "We would be denying history if we failed to recognize that Floridians today are in fact descendants of soldiers from both sides of the war. That's why I offered to issue a broader 'Civil War Heritage' proclamation -- one that would promote the discussion of the causes and effects of the Civil War from all perspectives."
Bush copied several aides on that response, one of whom noted that the Union Army had organized two regiments of cavalry from Florida.
"So even though the majority of Floridians sided with the south, Florida residents fought on both sides of the war," wrote Bush aide Cory Tilley. "And as you can see there were actually Florida veterans who fought for the union."
"Long live the union," Bush wrote in reply. "Abe Lincoln would be proud and he was probably our greatest presidente [italics added]."
Rarely, Bush received e-mails complimenting him for his decision to remove the flag and to stop recognizing Confederate Heritage Month.
An NAACP chapter wrote Bush in Sept. 2002 to thank him for his decision on the flag, but noted that some counties still flew it outside courthouses.
"I can only change policies directly as it relates to state government," he wrote back. "You are correct that I lead on this issue by removing the flags, other than the American flag and the beloved Florida flag on the state capitol premises.
"I can lead by example for the rest of the state," he added. "I have done so by embracing diversity and having no tolerance for racial hatred. My record has lost me support but it is the right thing to do."
Rosalind S. Helderman contributed to this report.