The earliest mention of Jews in Merkinė is dated 1539, when a dispute was adjudicated (July 8) between a Jew named Konyuk and a Christian in regard to a debt of the former.
In 1551 the Jews of Merkinė were named among those of fourteen other towns to be exempted from the special tax levied upon all inhabitants, with the exception of villagers and Jews, at the Lithuanian diet (Seimas) held in that year on November 27 at Vilnius.

In 1897 Jews made up 73% of the population of the town, and the community numbered 1,900.
From the 19th century through the period of Lithuanian independence, the Jewish community was very established and had numerous community organizations and institutions.
Following World War I, there was a very active Zionist movement and multiple Zionist organizations had offices in the town.

Merkinė produced in the 19th century some noted Hebrew scholars, as Mordecai Melzer, Isaac Magolis (d. New York 1887), and his son Max Margolis, of the University of California.

On September 10, 1941, 854 Jews from Merkinė, as well as from Liepalingis, Liškiava, and Seirijai were shot in a grove near the Jewish cemetery by German Nazis and their Lithuanian collaborators.

A mass grave of Jews killed during the Nazi occupation is in the forest behind the town.
The earliest mention of Jews in Merkinė is dated 1539, when a dispute was adjudicated (July 8) between a Jew named Konyuk and a Christian in regard to a debt of the former. In 1551 the Jews of Merkinė were named among those of fourteen other towns to be exempted from the special tax levied upon all inhabitants, with the exception of villagers and Jews, at the Lithuanian diet (Seimas) held in that year on November 27 at Vilnius.
In 1897 Jews made up 73% of the population of the town, and the community numbered 1,900. From the 19th century through the period of Lithuanian independence, the Jewish community was very established and had numerous community organizations and institutions. Following World War I, there was a very active Zionist movement and multiple Zionist organizations had offices in the town.
Merkinė produced in the 19th century some noted Hebrew scholars, as Mordecai Melzer, Isaac Magolis (d. New York 1887), and his son Max Margolis, of the University of California.
On September 10, 1941, 854 Jews from Merkinė, as well as from Liepalingis, Liškiava, and Seirijai were shot in a grove near the Jewish cemetery by German Nazis and their Lithuanian collaborators.
A mass grave of Jews killed during the Nazi occupation is in the forest behind the town.
Merkinė