Jews settled in Merkinė around the 16th–17th century. By the end of the 19th century, they made up about 74% of the town’s population. In Yiddish, they called Merkinė Merec or Merech. The Jewish community lived around the central market square and on nearby streets: Vilniaus, Kauno, Nemunaičio, and Seinų. Eyewitnesses recall that the square was surrounded by Jewish-owned buildings: homes, small shops, workshops, and even a restaurant.

In early September 1941, all Jews from Merkinė were herded into synagogues and the local school, where they were held for several days. Young men were selected and taken away first, followed the next day by young women and girls. Some of Merkinė’s Jews were deported to Alytus, while others from Liškiava and Seirijai were brought to Merkinė.

On September 10, 1941, the Jews of Merkinė were executed. In a small pine forest beyond the cemetery, they were stripped of their clothes, forced into trenches, and shot. The executions began with the young men, followed by women, children, and the elderly. In total, 223 men, 355 women, and 276 children were murdered at this site. Today, this place serves as a mass grave and a memorial to the victims of the Holocaust.