The synagogue was discovered in the mid-1960s by farmers from Kibbutz Ein Gedi while plowing the fields. The excavations took place at the beginning of the 1970s, and exposed a beautiful large mosaic floor, from the late Roman and Byzantine Eras. The synagogue served the worshipers between the 3-6 centuries CE, during which several changes and improvements took place.

The synagogue provides deep insight in to the life of the town it served and its inhabitants. Among the many archaeological finds discovered here was a scroll from the book of Leviticus and a bronze seven-branched menorah.

Ein Gedi was extremely prosperous: No other contemporary synagogue could boast the artistry, simple elegance, and precise execution of this mosaic (and there are plenty of others in Israel that remain from the same era). For a small, remote settlement of no more than a few hundred people to bring the best artisans in the country to create such a masterpiece would have cost a king’s ransom.

circa

Structure
The present structure is dated to the 5th century CE and based on earlier structures starting from the beginning of the 3rd century. The synagogue was destroyed by fire in the middle of the 6th century CE, during the period of Justin II.

Like the surrounding village structure was constructed of small roughly hewn boulders and fieldstones covered in plaster. Hirschfeld suggests that the synagogue was roofed with red tiles, although in preliminary reports the excavators do not mention any roof tiles from the synagogue structure. This assumption is most likely based on the depiction in Madaba Map, which depics red roofs on the buildings of En-Gedi.

circa

Central Mosaic
The central mosaic dates back to the Byzantine period, including a Judeo-Aramaic inscription mosaic now on display at Jerusalem's Schottenstein campus museum warning inhabitants against "revealing the town's secret" – possibly the methods for extraction and preparation of the much-prized balsam resin, though not stated outright in the inscription – to the outside world.

Respecting the Jewish tradition of refraining from figurative depiction, the decorations are based on geometric forms brilliantly weaved together to create a central 8-pointed star. The only living figures are geese and peacocks, inferior enough not to be associated with Roman gods.

The major element in similar contemporary synagogues is a central circular zodiac (an example would be Beth Alpha Zodiac) with the 12-star signs, each representing a Hebrew lunar month and a traditional personification of the four seasons, but with an image of the Greek god Helios seated in a chariot in the middle. In the Ein Gedi synagogue, however, we find a unique representation in a written list of the star signs, in a rectangular ‘carpet’ set on the floor of an aisle. This uncommon decoration reflects a different kind of community that adheres to tradition whilst the rest seem to give in to the ‘modern’ Roman aesthetics of the era.