Clysma was founded or rebuilt by Emperor Trajan in the second century AD to protect travellers and merchants as it lay at the junction of roads from Sinai, Palestine, and Egypt.

[2] This was done in conjunction with the construction of the Amnis Traianus, a canal that linked the Nile and the Red Sea and had its outlet near Clysma.

[9] The destruction of the Nile emporium of Koptos, from where goods were transported overland to Berenice and Myos Hormos, by Emperor Diocletian in the late third century temporarily disrupted trade at the southern ports and led to an increase of trade at Clysma which reached its peak in the fourth and fifth centuries.

[11] The Plague of Justinian likely first entered the Roman Empire through the port of Clysma, and thus spread to Pelusium, where it was first reported in mid-July 541.

[9] In c. 570, Clysma was visited by the anonymous pilgrim of Piacenza, who noted eighteen or more tombs of hermits at the city's basilica.