Persecution was the systematic maltreatment of individuals who fell into certain groups, such as followers of a religion or members of a species. One who believed they were being persecuted with little or no valid evidence to support their claims was said to have a persecution complex.
In 2268, Koloth demanded James T. Kirk deliver an official apology to the Klingon High Command, in which he took personal responsibility for persecuting Klingons in the quadrant surrounding Deep Space Station K-7. (TOS: "The Trouble with Tribbles")
Also that year, Lokai assured Pavel Chekov he couldn't possibly understand what it was like for him on Cheron, as Earth had no persecution. Chekov then recalled reading about persecution in Earth's past in his history class. Hikaru Sulu added that it had happened in the 20th century and that such "primitive thinking" had long since ceased. (TOS: "Let That Be Your Last Battlefield")