Anti-Semitism was virulent in pre-war Romania. Once war began, the continuing persecution of Romania's Jews culminated in mass murder. Romanian troops rivaled Nazi Einsatzgruppen in the brutal killing of Jews, annihilating about half of greater Romania's prewar Jewish population of 760,000.  According to the report of the International Commission on the Holocaust in Romania released in 2004, between 280,000 to 380,000 Jews were murdered in Romania and the war zone of Bessarabia, Bukovina and Transnistria.

During the 1930s, economic depression fueled Romanian propaganda that depicted Jews as parasites. Stringent laws stripped Jews of civil rights. In January 1941 Iron Guard Legionnaires stormed the Jewish section of Bucharest, where they burned shops, homes, and synagogues. Thousands of Jews were beaten and tortured. Some Jews were herded into a slaughterhouse and literally butchered according to Jews' own ritual practices of animal slaughter. The bodies were hung on meat hooks and displayed with "Kosher meat" labels.

The German invasion of the Soviet Union sparked further pogroms. In the recaptured Romanian provinces of Bukovina and Bessarabia, Jews bore the brunt of the killing frenzy. An estimated 250,000 perished there through mass shootings, through drowning in the Dniester River, or from starvation and disease within ghettos and slave-labor camps. In 1941, following the advancing Romanian Army after Operation Barbarossa, and alleged attacks by Jewish "Resistance groups", Romanian dictator Ion Antonescu ordered the deportation to Transnistria of all Jews of Bessarabia and Bukovina (between 130,000 and 145,000), who were considered en masse as "Communist agents" by the official propaganda. Transnistria, a southern Ukrainian territory located between the Dniester and the Buh Rivers was a Romanian military occupation zone. It became one big penal colony for Bessarabian and Bukovinian Jews, as well as the Jews from the Dorohoi district of Romania.

The Jews of Old Romania or Old Kingdom were spared - the Romanian government under Ion Antonescu considered them for barter as the war progressed and German victory become elusive.

Romanian soldiers also worked with the the Einsatzkommando, German killing squads, tasked with massacring Jews in conquered territories. Romanian troops were in large part responsible for the Odessa massacre, a mass killing of the Jews of Odessa and from the surrounding area in which between 25,000 and 34,000 Jews were shot or burned alive in the city. On October 22, a bomb detonated in the Romanian HQ in Odessa, killing 67 military personnel including the Romanian commander, 16 other Romanian officers, and 4 German naval officers. Blaming the Jews and the communists for the explosion, on October 23 the Romanian troops began the slaughter of 5,000 Jews in Odessa, first shooting them in groups of 30-40 or hanging them.

In the afternoon, more than 25,000 Jews were assembled and taken out to the gates of Dalnik. When they reached the gates, 50 people were moved into the trenches and shot by Lieutenant-Colonel Nicolae Deleanu himself. The Romanians were concerned that the killing would take too long a time and moved the rest of the Jews (approximately 22,000) inside four large storage buildings in which they made holes for machine guns. The doors were closed and Lieutenant-Colonel Nicolae Deleanu ordered the soldiers to fire into the buildings. In order to make sure that nobody had survived, they set the buildings on fire at 17:00 hours. The next day grenades were thrown into one of the buildings. Other Jews were herded into the harbor square, sprinkled with gasoline, and set on fire. Over 22,000 corpses were found in mass graves after the war.  Einsatz squads even complained of the Romanian soldiers' "undisciplined killing zeal," particularly their disregard for the disposal of corpses.

On August 23, 1944, just as the Red Army was penetrating the Moldavian front, King Michael led a successful coup with support from opposition politicians and the army. Michael, who was initially considered to be not much more than a figurehead, was able to successfully depose the Antonescu dictatorship. The Romanian Army ended the war fighting against the Wehrmacht alongside the Red Army in Transylvania, Hungary, Yugoslavia, Austria and Czechoslovakia, from August 1944 until the end of the war in Europe.

Romanian Holocaust historian Matias Carp writes: “Historical facts must be disclosed. If a percentage rate cannot form the basis of such a study, absolute numbers must be taken into account. When Romania was liberated from fascist tyranny, there were approximately 300,000 Jews alive within Romanian borders, and approximately 68,000 beyond the borders. This is the miracle.”