We still do not know what happened to Pantalica after the 8th century BC, when all traces of the prehistoric village disappeared, perhaps due to a war during the foundation of the city of Syracuse.
The site was inhabited again many centuries later, in two periods of history: around the 6th century AD, in the Byzantine period, and in the 9th century AD, during the Islamic raids in Sicily.
At this stage many of the funerary chambers that had been dug into the rock were enlarged and used as dwellings or churches.
New villages were born: the first was located near the Cavetta necropolis and had around seventy houses distributed around the Oratorio del Crocifisso (Crucifix Oratory); a second village was founded in the cliffs below the Anaktoron and its religious centre was the oratory of San Nicolicchio.
Lastly, the largest of these villages was located between the southern necropolis and the Pass of Filiporto and consisted of more than 150 houses and a small church dedicated to San Micidiario.