During the biblical period, Ein Gedi and the surrounding desert, known as the Wilderness of Ein Gedi, were part of the territory of the Tribe of Judah. David sought refuge from King Saul at Ein Gedi. (1 Samuel 24:1)
The first permanent settlement was built on the low hill, Tel Goren, at the end of the monarchic period (second half of the 7th century BCE). The houses of the small village were built close together on terraces; each consisted of two rooms and a courtyard. In them were large clay vats for the storage of drinking water or liquids made from special plants growing in the area. Royal seal impressions, and others bearing personal names, as well as a hoard of silver pieces were found in the ruins of the village, indicating wealth and economic importance.
During the Persian period (5th-4th centuries BCE) the village grew in area. Among the buildings was a prominent, large structure (550 sq.m.), probably two stories high. It had many rooms, courtyards and storerooms in which numerous artifacts, including royal seal impressions were found. These attest to the continuing importance of the village.
In the Hasmonean and Herodian periods (first century BCE to first century CE) the Jewish settlement at Ein Gedi thrived, expanded and became a royal estate. At Tel Goren, a well-fortified citadel was built to protect the village and its agricultural products against raiding nomads. At this time Ein Gedi expanded and spread to the low, flat hill at the foot of Tel Goren. Ein Gedi was destroyed and abandoned during the First Jewish Rebellion against Rome (66-70 CE).
In renewed excavations, beginning in 1996, some 30 stone-built cells, clustered around a small spring, were found northwest of Tel Goren. The excavator suggests that this might have been a monastic site of the Essene sect, whose members lived in isolated communities in the desert near the Dead Sea during the Roman period.
During the Bar Kochba Revolt (132-135 CE), Ein Gedi was an important outpost of the rebels, as recorded in the Bar Kochba letters found in the Dead Sea area. Later, a Roman garrison was stationed at Ein Gedi.
During the Roman and Byzantine periods (2nd-6th century), the oasis was an imperial estate and the settlement at En-Gedi reached the peak of its prosperity. Eusebius, 4th century bishop of Caesarea, describes Ein Gedi as a "very large Jewish village." In the course of excavations, remains of dwellings, water installations and shops along streets, were uncovered. During this period, stone terraces were constucted on the hillsides and a sophisticated water system, including storage pools and a network of irrigation channels, was developed. These measures, initiated by the central administration, made for expanded, efficient and intensive cultivation of tropical plants and the production of perfumes and medicines. Especially famous and costly was Balsam, a perfume produced from a plant that grew only in this region. To protect the cultivated areas and to control the trade route, a fortress and watch towers were built.
The synagogue at Ein Gedi dates from the Roman-Byzantine period, but it underwent several changes in the course of its use.
When first built at the beginning of the 3rd century, it was a modest, trapezoidal structure. In its northern wall, facing Jerusalem, were two openings. The floor was of simple white mosaic with a swastika pattern in black tesserae in the center. This pattern has been interpreted as a decorative motif or as a good luck symbol.
The synagogue underwent far-reaching renovations during the fourth century: The opening in the center of the northern wall was blocked and made into a square niche which probably contained a wooden Torah ark; along the opposite southern side a three-stepped bench was built; the building was divided by two rows of square pillars into a central hall with two aisles; the entrance was through three openings in the western wall.