The earliest written references to Jews in Markvarec date back to the first half of the 18th century.
A Jewish community was founded most likely in the second half of the 18th century, but it was dissolved in 1888 due to the small number of members. Jewish houses were centered around the synagogue from the 18th century and formed a ghetto in the southeastern part of the village near the creek. Most of the original twelve houses have been reconstructed but still stand.
The synagogue was built in Baroque style in the years 1784-1786 and served for worship until the end of the 19th century. After the war it collapsed and the remnants of the walls were removed in 1992.
The Jewish cemetery was founded in 1794 and is located one kilometer southeast of the village in the forest. The oldest surviving readable tombstone dates back to 1802 and belongs to a person named Moshe. Although the last Jewish family moved out in 1927, Jews from the surrounding area, especially from Dačice, were buried in the cemetery until 1939. About 240 tombstones have been pre-served over 1,223 square meters. The entrance to the cemetery is by the morgue from 1908, which has been recently repaired.