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The history of the Jews in Kyrgyzstan is linked directly to the history of the Bukharan Jews of Uzbekistan. Until the 20th century, most Jews living in the Kyrgyz areas were of the Bukharian Jewish community. However, during the 20th century, large amounts of European Jews began to emigrate to Kyrgyzstan which was then part of the Soviet Union, and a small amount of them still live in the country.
Archeological findings suggests that Jewish traders from Khazaria started visiting the Kyrgyz territory around the 6th century CE.
In Kyrgyz tradition, the term "Djeet" similar to e.g. Polish żyd was used in order to describe Jews, and it is mentioned in the Kyrgyz epic poem Manas, which dates back to the 10th century CE. In Manas, several central-Asian cities are described as having Jewish communities in them, among them Samarkand, Bukhara and Baghdad, though none of them have ever been inhabited by a majority of Kyrgyz people nor included in a Kyrgyz territory.
According to a census held in 1896, the Jews represented about 2% of the region total population. It can be assumed that almost 100% of these Jews were Bukharian Jews or at least Sephardic Jews, meaning no Ashkenazi Jews were living in the Kyrgyz area before the 20th century. During World War II many Jews fled from the European parts of the Soviet Union to central Asia, including Kyrgyzstan, making the Jewish community of Kyrgyzstan combined out of an Ashkenazi community and a Bukharian Sephardic one. The two communities functioned separately and though it did occasionally happen, Ashkenazi–Sephardi intermarriages were not common.