While the civil war is associated with the end of slavery in the US, the so-called peculiar institution survived throughout much of the Confederacy right to the end of the conflict. That’s the thought-provoking narrative of a comprehensive new book by Robert KD Colby, a history professor at the University of Mississippi.

“Many Confederates saw slavery as indelibly bound up with their bid for independence, and used the slave trade to try to build a world around an independent slaveholding republic,” Colby says.

In An Unholy Traffic: Slave Trading in the Civil War South, Colby cites a shocking statistic. Between 80% and 85% of people enslaved in the Confederacy on the eve of war in 1861 were still enslaved when Gen Robert E Lee surrendered in Virginia four years later. The number of Black people who were bought and sold over that span is estimated in the thousands.

And the Confederacy didn’t merely defend slavery within its borders.

“Essentially, anytime the Confederacy invaded a place where slavery was either more tenuous or people had fled from slavery, it absolutely took people back into slavery … many times, people who had not been enslaved at all,” Colby says.

Colby first came across hints of the overall story when he was a PhD student at the University of North Carolina, about a decade ago. That time period coincided with an outburst of scholarship on the domestic slave trade and capitalism. But while he admired such historians’ insights, Colby noticed that most such narratives ended with the civil war. This was understandable: slavery was tied to the cotton economy, which was destroyed by the war. Yet something prodded Colby to look into slavery during the war and what he found surprised him.

“I just found example after example, moment after moment, of people being bought and sold,” he says. “The more I read, it seemed to coalesce into broad themes,” including “how people experienced the civil war, how the slave trade shaped Confederate expectations of what their project was supposed to do, and how enslaved people pursued freedom during the war”.

As Colby explains, the slave trade underwent a reorientation. The antebellum practice was to sell enslaved people from the upper south to the lower south and the so-called “Cotton Kingdom”. Early in the war, this was no longer possible due to the Union capturing major markets such as New Orleans, Natchez and Memphis. Thus, enslaved people were sent to places where confidence in the south ran high.

The Confederate capital, Richmond, was prominent on that list, along with the original capital, Montgomery, Alabama. In another Alabama city, Mobile, slave traders advertised their heinous industry with an 1863 travel guide. Those engaged in the trade included major firms such as the Richmond-based Hill, Dickinson & Co and also ordinary citizens, such as an Alabama husband and wife, Nimrod and Queen Long, who debated selling an enslaved woman, Ellen, during a brief moment of Confederate military resurgence.

“For the most part,” Colby says, the trade “persisted in the places where the Union forces weren’t. It was squeezed into smaller and smaller areas. In those areas, it continued, for a variety of reasons.”

Where there were shortages of food, enslaved people might be sold to avoid “excessive mouths to feed”. When conscription into the army caused labor shortages, enslaved people could be acquired to “make up the difference”.

“Of course, plenty of people’s desire to continue buying and selling enslaved people was shaped by the degree of faith they had resting on the Confederacy. Confederates [bought] enslaved people almost as a bet on the prospect of Confederate victory.”

Colby addresses the grim narrative of women and children who Confederates anticipated would have a lifetime of labor and child rearing in a postwar nation. Colby sees the narrative of Kate Drumgoold as an example. When she was about eight, her enslaver in Virginia turned down what Drumgoold recalled as an unprecedented offer to sell her. But two of her 10 sisters were sold, as was their mother.

Despite the formidable apparatus of slavery, Black people found ways to resist, notably by escaping, as in the case of Mary Pope in Virginia. Pope’s husband, Joe Dardin, had been sent to slave traders early in the war. When her enslaver threatened to sell Pope and her four children too, the family fled to a Union camp for freedmen in the port of Norfolk. In Charleston, South Carolina, the hub of secession, William Summerson and his wife knew it was time to escape once they were appraised for sale. Hiding in barrels, they made their way to a Union gunboat.

“There was not one story of emancipation but thousands of smaller stories, thousands of individual stories of how people chose to pursue or chose not to pursue freedom during the war,” Colby says. “I hope the book speaks to just how complex the process of African American pursuit of freedom was during the civil war, and the magnitude of obstacles standing in the way – including and not limited to the threat of being captured and sold as they pursued their freedom.”

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The Confederacy was not the only place where slavery existed during the war. It also existed in the loyal “border states” of Delaware, Maryland, Missouri and Kentucky. Here too there was a reorientation away from the lower south. Colby estimates that hundreds, perhaps thousands of enslaved people were sent from Missouri, which was rent by violence, to Kentucky, which was largely undisturbed in the final years of the war.

As the Union made deeper gains, the pace of emancipation accelerated. Colby documents the impact of Gen William T Sherman’s capture of Atlanta and march through Georgia in 1864. Union forces liberated enslaved people from jail; members of a coffle freed themselves from the traders Blount & Dawson. Yet the domestic slave trade continued into the war’s final moments.

Hill, Dickinson & Co made more than $1m from selling enslaved people between October and December 1864. A Virginia trader, Robert Lumpkin, attempted to bring 50 enslaved men, women and children out of Richmond in its last days as the Confederate capital. Lumpkin sought to transport the group for future sales, wherever Lee’s army might find refuge.

Colby chronicles the triumph of emancipation – and the future life of freedmen. Many sought to reunite with family members who had been sold into slavery. Sometimes they were aided by the newly established Freedmen’s Bureau. There were success stories: Kate Drumgoold vividly recalled a reunion with her mother. Others, however, issued calls for lost loved ones for decades after the war.

Colby notes that in attempting to reunite their families, formerly enslaved people sometimes sought help from the very people who might have once enslaved them: former slave traders.

Of the latter, he says, “Some were deeply spiteful and resentful of the way the war destroyed their business … [but] I found one or two who were actively helpful in the process of reuniting families. I think it speaks to, on the one hand, the opportunities that the end of the war and emancipation provided to formerly enslaved people, and also the limitations of this.”

• An Unholy Traffic is published in the US by Oxford University Press