The revolts were marked by great violence on both sides, and their brutal suppression at the hands of the Byzantines and their Ghassanid allies severely reduced the Samaritan population.

The events irreversibly shifted the demographics of the region, making the Christians the only dominant group in the Palaestina Prima province for many decades onward.

This period of semi-independence was brief, however, as Byzantine forces overran Samaria and took Baba Rabba captive to Constantinople, where he died in prison several years later around 362 CE.

The Emperor went to Neapolis, gathered the elders and asked them to convert; when they refused, Zeno had many Samaritans killed, and rebuilt the synagogue into a church.

Later, in 484, the Samaritans revolted, provoked by rumors that the Christians intended to transfer the remains of Aaron's sons and grandsons Eleazar, Ithamar and Phinehas.

[5] According to John Malalas, Asclepiades, the dux Palaestinae (commander of the province's Limes Arabicus troops), whose units were reinforced by the Caesarea-based Arcadiani of lestodioktes (police chief) Rheges, defeated Justa, killed him and sent his head to Zeno.

[8] Some modern historians believe that the order of the facts preserved by Samaritan sources should be inverted, as the persecution of Zeno was a consequence of the rebellion rather than its cause, and should have happened after 484, around 489.

Zeno rebuilt the church of Saint Procopius in Neapolis and the Samaritans were banned from Mount Gerizim, on whose top a signaling tower was built to alert in case of civil unrest.

[9] Following massive riots in Scythopolis and Samarian countryside, the rebels quickly conquered Neapolis and ben Sabar emerged as their leader, being proclaimed a king.

[citation needed] As a response, forces of the dux Palaestinae, combined with units of local governors and the Ghassanid Arab phylarch, were dispatched to deal with the uprising.

[11] The forces of Emperor Justinian I quelled the revolt with the help of the Ghassanid Arabs; tens of thousands of Samaritans died or were enslaved, with their death-toll possibly being between 20,000 and 100,000.

Emperor Justin II (r. 565–578) complained about "outrages committed by....Samaritans at the foot of Mount Carmel upon the Christian Churches and the holy images".

[citation needed] Samaritan numbers remained very low in the Islamic era, similar to the late Byzantine period – a result of previous revolts and forced conversions.

[16] Contemporary sources claim 30-80,000 Samaritans were living in Caesarea Maritima prior to the Muslim invasion (alongside roughly 100,000 Jews), out of a total provincial population of 700,000 of mostly Christians.

[19] Islamic religious leaders also periodically sought to consolidate their power by stirring up anti-Samaritan sentiments and occasionally calling for their annihilation.