The Confederate flag flies high next to a number of governmental buildings across Baton Rouge: the federal courthouse on Florida Boulevard, the State Archives on Essen Lane. It’s also displayed behind the City Hall building and at the walking entrance to the Mississippi Riverfront levee.

But if you missed it, that might be because it’s not the same flag most people have come to associate with the secession of the South during the Civil War. That is the battle flag, the flag flying at the South Carolina capitol, which this week sparked a national debate about whether a symbol so closely tied to slavery and decades of segregation endured by black people should be flown over government buildings.

Baton Rouge institutions instead are flying what is frequently called the “Stars and Bars,” the original flag of the Confederacy, adopted in 1861, with a circle of white stars in the top left corner and three wide stripes. Across the city, it is flown alongside other flags of the countries that ruled this territory, from France to the Republic of West Florida.

Over the past week — since the shooting that claimed the lives of nine black worshippers at a historic Charleston church — leaders across the deep South have embarked on fresh reconsiderations of Confederate symbols in public spaces. South Carolina’s governor called for removal of the flag at the capitol, while the Republican Speaker of the House in Mississippi came out in support of removing the Confederate imagery incorporated into that state’s official emblem.

Some New Orleans leaders are now questioning the monuments that dot that city’s landscape, from the statue of Gen. Robert E. Lee at a prominent intersection to another in honor of Confederate President Jefferson Davis, placed on a landscaped street that also bears his name.

Baton Rouge civic leaders engaged in their own debate about the Confederate flag 20 years ago, ending with a compromise that at the time satisfied all sides.

In 1994, the city and federal courthouse both flew the more recognizable and controversial battle flag, featuring a blue “X” with white stars over a red background. But some black leaders objected, saying it was a symbol not just of the Confederacy, but of the state’s white supremacist history until the civil rights era. In response, the city and federal court leaders changed out the flag, opting for the more historically accurate “Stars and Bars,” which would have been the only Confederate flag flown in Baton Rouge until Union troops captured the city in 1862.

Chief U.S. District Court Judge Brian Jackson said the compromise to replace the flag was made long before he became a judge and he did not have an opinion on the banner that flies outside the federal courthouse today.

But he said he’s not aware of any complaints that have been made about the flag since it was swapped out.

Mayor-President Kip Holden did not respond to a request for an interview for this story.

His aide, Scott Dyer, noted Tuesday that the Confederate flag is not currently flying at City Hall or on the levee because of the Charleston shooting.

“The mayor ordered the American flag to be flown at half-mast last Friday in memory of the Charleston shooting victims, and when that happens, all of the other flags are removed,” Dyer said in an email.

Davis Rhorer, executive director of the Downtown Development District, said the Confederate flag is displayed within a historical context.

“It shows all the different countries and entities that were over this part of Baton Rouge,” he said. “This is one of the lineup.”

Rhorer said he thinks the decision to use the “Stars and Bars” flag is less emotional for people.

“I think the symbolism is pretty strong when you see that (Rebel flag),” Rhorer said.

Thomas Taylor, a commander of the Louisiana Sons of Confederate Veterans, said the Confederate flag, even the battle flag, has been twisted into a symbol of racial hatred by people with a political agenda. But he said the flag is a symbol of Louisiana and other Southern states’ proud heritage.

He said he’s frustrated to see the debate about the flag emerge from a tragic killing that he said is completely unrelated, although South Carolina shooting suspect Dylann Roof displayed photos of himself with the flag and a gun.

“This is a knee-jerk reaction to what happened in South Carolina,” he said. “It had to do with some nut who took it upon himself to kill those people, but it had zero to do with the battle flag. … We don’t want anything to do with him.”

But some Metro Council members said the national debate should send a signal to Baton Rouge that it is time to re-evaluate its symbols.

“Do I think it needs to come down in public buildings, given what’s transpiring throughout the nation; I’d say yes,” Councilwoman C. Denise Marcelle said. “People need to know their history, but there are other ways to do that.”

Councilwoman Tara Wicker admitted she had previously not taken much notice of the flags, because they’re not as recognizable as the battle flag.

But she said she is still concerned the flag is associated with a time of oppression for African-Americans.

“I know it’s a part of history, but a lot of it is an unfortunate part of history for a large segment of our population,” she said. “We want to make sure we’re sensitive to what that history means to other people.”

But flags are hardly the only reminder of Confederate influence in Baton Rouge.

Like many places across the South, Civil War references can be seen on street names, buildings and schools.

Until a few years ago, a statue of a Confederate solider was displayed on a downtown street, near City Hall. It was not particular to one soldier, but rather a tribute to all Confederate soldiers.

The statue was moved in 2012 to the Old State Capitol when downtown construction started on North Boulevard Town Square. It’s currently on loan to the West Baton Rouge Museum until Aug. 16. The plaque says the statue was erected as a tribute to “the heroism and patriotic devotion of the noble soldiers from the two parishes (East and West Baton Rouge) who wore the gray and crossed the river with their immortal leaders.”

When the statue was on the street, Rhorer said he received a few complaints from people who said they were offended by it. But once it moved to the Old State Capitol, a museum of Louisiana history, the issue was resolved.

Elsewhere in Baton Rouge, one of the more prominent reminders of the Confederate past would be Lee High School. It is officially Robert E. Lee High, named after the famed Civil War general, but the school’s literature these days drops the “Robert E.”

The school, which first opened as an all-white school in 1959, for decades played as the Rebels, complete with a Col. Rebel mascot. In 2005, after the student population shifted from mostly white to mostly black, students voted to change the mascot from the Rebels to the Patriots.

School Board member Barbara Freiberg, a graduate of Lee High, said she has talked to people through the years who don’t like the name, but those conversations are rare. She also pointed out that Lee High has active alumni, including black and white members, who have expressed in the recent past the desire to preserve the name.

At LSU, numerous buildings, including Kirby Smith Residence Hall and Thomas Boyd Hall, are named for Confederates, as is Raphael Semmes Street.

Khrystien Frelow, an LSU senior and member of the Black Student Union, said she sometimes feels conflicted walking around campus using facilities named for famed Civil War figures.

“I might feel more comfortable if I was walking on a street that’s not named after a person who wanted to hang me,” she said.

She and her friend, Anastasia Elie, another senior, said they don’t necessarily think the school needs to change the names of buildings and roads, but they’d like to see the administration be more vocal about the use of rebel flags by students, particularly during football season.

“If we want to have a welcoming institution and be a welcoming environment, then we can’t have these racially charged flags displayed on the tailgate,” Elie said. “How does it look for a tailgate with a Confederate flag to be cheering on a predominantly black team? It’s a double standard.”

Local Baton Rouge historian Tim NesSmith said it’s impossible to wash away Civil War references from Baton Rouge, noting that the capital city was the site of a major battle and located near other major battles.

He said Baton Rouge and other Southern states can embrace their history without glorifying the parts that are offensive to others.

“Everything has to be in context,” he said. “Having the Stars and Bars battle flag flying over a governmental complex might not make as much sense as having it in a museum exhibit discussing the actual conflict.”

Advocate staff writers Terry Jones, Charles Lussier and Jaquetta White contributed to this report.