After its re-foundation by Charles of Anjou in the XII century, Mola then passed its ups and downs and retained the status of state town, almost continually, until the early fifteenth century. According to some local historians, this was a period of relative prosperity for the town, whose population recorded a significant increase. Virtually painless was the descent in Southern Italy of the Hungarian army of Louis I in 1348, to whom the local population immediately declared fidelity, saving the place from being looted, as it happened to neighboring centres.
With the passage of the Kingdom of Naples from the Angevins to the Crown of Aragon, the indebtedness of the Crown determined the sale of state property to the creditors. Mola thus lost the status of a free city and was subjected to different feudal lords: the Gesualdo from 1417, the Maramaldo from 1435 and the Toraldo from 1464.
In 1495, with the arrival in Italy of Charles VIII of France to claim the Kingdom of Naples, Mola, along with other ports in Apulia, was ceded by the Aragonese to the Republic of Venice, in exchange for a huge loan. Venice wielded repeatedly the city, but was never able to conquer the city castle, which remained loyal to Naples. With the period of Venetian rule, which lasted until 1530, Mola strengthened ties with the other side of the Adriatic and recorded an overall economic progress.
Back again under Toraldo and then passed to the Carafa, in 1584 the people from Mola managed to collect the considerable sum of 50,000 ducats that allowed them to break free from the feudal yoke to be subject only to the royal property. Soon, however, the estate was bought by Antonio Carafa, a few years later forced to sell it at auction to pay his debts.