The Jews in Uzbekistan were affiliated with two communities: (1) the ancient one, the Jews of Bukhara, who speak a Tajiki-Jewish dialect; (2) the new one, of Eastern European origin.

According to their tradition, the Bukharan Jews emigrated from Persia at the time of the persecutions of King Peroz (458–485), while some consider themselves as descendants of the exiles of Samaria, on the assumption that "Habor" (II Kings 17:6) is Bukhara. Anthropological examinations undertaken by L. V. Usbanin in 1926–29 proved that they originated in the Middle East (of the pure Armenoid type), although there is no information on their exact non-Jewish origin. Precise information on the spiritual works of the Jews of Uzbekistan is, however, only available from the 14th century onward.

Jews of Uzbekistan emigrated to Khazaria and China because of their location at the crossroads of the caravans that traveled there. The principal traffic between the Muslim world and Itil (Atil), the capital of Khazaria, passed through northern Uzbekistan, and the information on "many Jews who came to the king of the Khazars from the towns of the Muslims" (the author al-Masudi of the tenth century) and the Jews who came "from Khurasan and strengthened the hands of the inhabitants of the country" (the anonymous "Cambridge Document") refers essentially to the Jews of Uzbekistan, which was considered as an annexed territory of Iranian-Eastern Khurasan.

There is a tradition concerning another wave of Jewish emigration from Iran to Uzbekistan as a result of the Mongolian conquests of the 13th century, and the surnames of the Jews of Uzbekistan show that even during subsequent periods emigrants from Iranian-speaking communities of the west and the south were integrated among them. In modem times, however, the fanatical Muslim domination severely prejudiced the growth and economic development of the community. The Russian conquest of the 19th century came as a blessing, especially in those regions subjected to direct Russian rule, where the local Jews were granted complete judicial equality with the Muslim natives and enjoyed rights which the Russian government withheld from the Jews of Eastern Europe (such as the free acquisition of real estate). A migration movement from Bukhara to Tashkent continued through several generations. The economic progress of these Jews was also reflected by their considerable contribution to the Jewish settlement of Erez Israel. The Soviet regime, which liquidated private commerce, brought about the transfer of the more than 200,000 local Jews into administrative positions, industry and agriculture.