Jewish people were mentioned in many publications dating all the way back to XV century, however their permanent settlement was not until 1616. Permission for residing in Merkinė was given by the major of the town Jonas Vaina, a decision which made the King Vladislovas Vaza very angry. This, however did not stop the major and permission was granted.

Over the year several synagogues were constructed to appeal to Jewish beliefs and consequently Jewish cemetery was established also. Over second world war period Merkinė lost many of its Jewish citizens and in turn holocaust victims burial ground was created right next to the older Jewish cemetery.