By far the grandest ancient structure at Capernaum is the partly restored synagogue, which towers in white limestone above the basalt environs. On the basis of dates on some 30,000 coins (deliberately embedded, it would seem, in the mortar of the floor), Corbo and Loffreda dated the building to the late fourth century AD. Magness, however, holds that the embedding occurred in the sixth century and that the structure dates from that time at the earliest.

But how can we be sure that the later, white building is a synagogue? First, despite its unusual grandeur, the form and southward orientation are similar to those of several other synagogues in Galilee. Also, among the decorative elements exhibited in the grounds (whose exact position in the structure the restorers did not know), we find a seven-branched candelabrum carved (secondarily at an angle) on a capital, together with an incense shovel and a ram's horn. These three together functioned in antiquity as the primary symbol of Judaism. (The Star of David achieved its specifically Jewish connotation very much later.)

Some also like to identify a unique stone carving as the ark of the covenant, but it might better represent an imperial triumphal procession, in which a building (the Temple?) is being wheeled away. Yet why would Jews represent such a thing?