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The German army occupied Joniškis on June, 24 1941. Nationalists who took control of the town immediately started persecuting the Jews. The town's Jews, more than 400 men, women and children, were shot dead by the Nazi occupiers and their Lithuanians collaborators in two murder operations in July and August 1941. In 1943-44 the German authorities set up a forced labor camp which held more than 600 Jewish prisoners deported from the Vilna region.
In summer 1944 Joniškis was liberated from the Nazi rule by the Red Army.