First mentioned in 1359, Merkinė is one of the oldest Lithuanian settlements. It received the Magdeburg rights in 1569. The town is the location of The Mount of Queen Bona, a mound which was the site of an ancient hill-fort overlooking the rivers. Situated on a historic Warsaw–Vilnius trail, the town was also the place where King of Polnd And Grand Duke of Lithuania Wladislaus IV of Poland died in 1648. The mass grave of Lithuanian Jews killed during under Nazi occupation is in the forest behind the town.