Neandria was founded as a Greek colony by Aeolian settlers, most probably around 700 BC. From 454 to 431 BC the city was a member of the Delian League as Neandreies. In 399 BC it was incorporated into the Persian empire. The city history is relatively short, because around 310 BC Neandria was completely abandoned by its inhabitants who were resettled in the newly founded harbor city. The person responsible for this decision was Antigonus I Monophthalmus - one of the generals of Alexander the Great. After the death of the Macedonian king Antigonus became the ruler of the western Asia Minor. His goal, however, was to conquer all the lands once controlled by Alexander. His ambitions enraged the other Macedonian leaders who joined their forces and defeated him in the Battle of Ipsus in 301 BC.

Before his death Antigonus founded the harbor city Antigoneia, later known as Alexandria Troas. The inhabitants of Neandria were resettled there. However, the issue of the city walls that encircle Neandria remains one of the archaeological puzzles. There is some evidence that suggests that during the Persian rule the city was not fortified. The archaic walls surrounded the acropolis area only. The style of the walls encircling the whole settlement indicates that their construction took place in the early Hellenistic period, just before the abandonment of the city or even afterwards.

An interesting hypothesis has been put forward by F. E. Winter from the University of Toronto. According to his suggestions after the inhabitants of Neandria had been resettled to Alexandria Troas, the rulers of this region, Antigonus I Monophthalmus or the victorious general of the Battle of Ipsus - Lysimachus, decided to transform Neandria into a fortress. The strategic location of Neandria in the south-western Troas seems to confirm their motivation for this move. The mountain where Neandria once stood offers a great view over the valley of river Scamander (now Karamenderes) and the vast plain from the Dardanelles to the mouth of the river Satnioeis (now Tuzla Çay). In the turbulent times after the death of Alexander the Great the great tactical importance of such a well situated fortress was difficult to neglect.

The Winter's hypothesis is further confirmed by the reinforcement of the defensive walls and the erection in the central area of Neandria of evenly planned buildings (barracks) as well as the complete lack of any traces that could testify to the existence of the city (e.g. coins or graves) in this location after 310 BC. The civil buildings (a temple, an agora and a theatre) were neglected after this date.

However, even if a fortress existed in Neandria in the late 4th century or in the early 3rd century BC, it was also abandoned, in 280 BC at the latest. There are also some premises to believe that in Roman times a small settlement existed there. It would have had a connection with the nearby quarries where the marble has been acquired until today. From this Roman village no traces have been found so far.