During the period of Radical Reconstruction, the Ku Klux Klan emerged as a terrorist organization that sought to revert time and restore racial and labor relations to their ante bellum status. Unleashing a campaign of terror that has no equal in American history, the Klan used violence to repress Black political participation and keep them from economic equality, attacking African-Americans and White Republicans. These groups sometimes managed to organize and fight back, but by and large their efforts were not enough, and it wouldn't be until the vigorous execution of the Enforcement Acts by the Grant Administration that the power of the Klan's first iteration was broken.

As Eric Foner describes in his book, Reconstruction: America's Unfinished Revolution, certain groups fought against the Klan through vigilante justice. He gives several examples, such as the Anti Ku-Klux of Bount county, Alabama, a group formed by White Union veterans who stopped Klan violence through threats of retaliation. He also mentions a White Georgian who, disgusted with the Klan's actions, "singlehandedly fought off twenty attackers, killing four."

Freedmen also organized to resist Klan violence. In South Carolina, armed Blacks patrolled the streets of Bennettsville, while a mob of Freedmen lynched three whites accused of murdering a Black lawyer in Arkansas. The most prominent but also most tragic example of organized Black resistance took place in Colfax, Louisiana, where after a contested Governor's election, a group of Blacks led by Union veterans tried to fortify the county seat. They were soon overwhelmed by better armed Whites, who proceeded to massacre them indiscriminately. The Colfax Massacre, with around 150 victims, is a lamentable example of how much blood the Klan was willing to split in order to restore the South to White Supremacy, but also of how difficult it was for Blacks to resist effectively.

For one, Blacks were outmatched in training and equipment, since the Klan was better armed and was formed mostly of Confederate veterans. There were many Black Union veterans, but their numbers were dwarfed by the number of Confederates. Some Republicans also argued that Blacks were meek and feeble, not used to standing up to abuse by Whites due to a long story of slavery. Yet, White scalawags were just as reluctant to use violence sometimes. It seems that Republicans were just less willing to use extrajudicial violence against the Klan. One factor was, of course, the fact that the Klan enjoyed the support, both tacit and express, of a large section of Southern whites, who saw them as noble crusaders who fought to liberate them from Republican rule.

Southerner elites and Democratic politicians often openly supported the Klan, praising it for doing a "good" for society and saying that its activities were not politically motivated or that they were justified. Even men who disliked the Klan refrained from speaking against it publicly. The Klan also threatened witnesses or used violence to prevent the effective administration of justice. Under such circumstances it was almost impossible to successfully get an indictment, and even when one was produced, Southern juries would not convict. Consequently, in many occasions whites could indeed commit crimes against Blacks with impunity. Nonetheless, I must point out that under Radical Reconstruction Blacks were allowed to testify and present evidence, and the presence of sympathetic Republican officials, many of them Black as well, meant that going unpunished for violence against Blacks was becoming rarer, though enforcement of the law against Klan thugs was harder than against common criminals.

Republican state governments did try to enforce the law with a measure of fairness, it's just that people refused to cooperate because they did not "believe that the present state government is legitimate”, as William H. Trescot said. Laws passed by Southern Republican governments that raised penalties for murder or assault, prohibited using disguises or even required counties to indemnize victims of Klan violence, remained a dead letter due to the difficulties of enforcement. Republican overreliance on Federal patronage and factional disputes between conservatives who wanted to woo Whites and radicals who focused on the plight of African-Americans also contributed, for many Republicans were reluctant to enlist Blacks into the militia or appeal for Federal assistance. Some did organize militias more successfully, even managing to defeat the Klan. But altogether, it would not be until the Federal government intervened under the terms of the Enforcement Act that the Klan's reign of terror would be truly over, though by then Reconstruction had started to unravel.