The two main rooms are a prayer hall and an adjoining courtyard to its east. Under the central part of the prayer hall, the archaeologists discovered the pavement (now covered again) of another large building, which they date to the time of Jesus. In such a village, a lone public building would most likely have been a synagogue. It has always been the practice in this land, moreover, to erect a new shrine on the site of the old, since the spot itself is deemed sacred.  Standing in the middle of the prayer hall, then, one is near the setting of the stories in Mark 1 and John 6. 

But how can we be sure that the white building from the 6th century was a synagogue? First, despite its unusual grandeur, the form and southward orientation are similar to those of several other undoubted 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.)

That question may relate to another: It is a puzzle how the Jews of Capernaum could have dared to build so grand an edifice, with limestone imported from miles away, at a time of Christian emperors -- and with a modest but important church thirty yards to the south. People told Jesus that a Roman centurion funded the synagogue. Perhaps this later edifice too was financed by a foreigner: the Emperor himself, so that Christian pilgrims, seeking the sites of Mark 1 and John 6, would not be disappointed.