The German army occupied Alytus between June 22 and 24, 1941.
Local Jews, along with those from the neighboring towns of Varena, Butrimonys and Merkine, were forced into a ghetto formed in the town at the beginning of September 1941. SD officer Joachim Hammann, with the assistance of local Lithuanians, began to concentrate the remaining Jews in the poorest quarter. The Jews attempted to organize themselves in order to facilitate ghetto life, but frequent arrests, abuse and murders impeded their endeavors. The Jews of Alytus and some towns in the vicinity were the victims of a number of murder operations in July-September 1941. The first killings occurred at the beginning of July, when some Jews were murdered by Lithuanian nationalists, with the consent and participation of the German occupying forces. The ghetto was liquidated on September 9, 1941, when all its inmates were murdered.
The Red Army liberated Alytus on July 15, 1944.