Miletus was a city on the Aegean coast of Asia Minor. Its excavated remains show that Miletus flourished in the time of Diocletian, when much building and restoration took place, then fell into a decline. Ancient buildings collapsed and small, shoddy structures, which disregarded the regular urban plan, were constructed over and within the ruins. 
The reign of Justinian I brought recovery as shown by a new cathedral, restored baths, and drainage of the harbor, works owed to the influence at court of a native son, Hesychios of Miletus. Some major new buildings were constructed, such as the Episcopal Palace, with its fine recently-restored mosaics, beside the Church of St. Michael. However, often Hellenistic and Roman buildings continued to be used or were converted to new uses in the Byzantine period. For example, the Roman South Market gate still stood and was rededicated with the addition of a new inscription. The Church of St. Michael itself had been the Hellenistic Temple of Dionysos and was converted into a church on a basilica plan with an east–west orientation, three apsidal naves and a baptistry. The city must therefore have remained an impressive place, as most of its earlier public buildings remained in use, albeit designated with new functions. New fortification walls of the 7th-8th century, which excluded much of the ancient city and used the theater as their citadel, indicate a drastic contraction. Suffragan of Aphrodisias, Miletus became an autocephalous archbishopric by 536, and a metropolis under Manuel I. 
From the thirteenth century AD onwards, Miletus came to be known as Palatia, ‘The Palaces’, although this is probably a reference to the ‘palaces’ of an earlier era that could be seen all around it, rather than to new palaces of the Byzantine period itself. The Byzantine castle, situated directly on top of the theater that now dominates the site of Miletus was built in the sixth century AD. With ten towers and centered around a courtyard, it has commanding views over all of the city and harbors below it. Eventually, perhaps in the 12th century, Miletus withdrew entirely within the theater citadel. While the Lion Harbor had become completely clogged with silt and was unusable, the Theater Harbor probably remained a serviceable harbor but Miletus was rapidly losing ground as a port. The city was increasingly on the periphery of the Byzantine world as the empire contracted towards Constantinople in face of the advancing Muslim forces of Anatolia. In 655 AD the new Islamic fleet defeated the Byzantine fleet in the Battle of the Masts off the coast of Lycia, thereby marking the end of Byzantine naval power in the eastern Mediterranean. 
Miletus (now called ‘Balat’, a derivation of the Byzantine name Palatia) was taken by the Menteşe emirate in 1261 AD, in a region that was hotly disputed between competing emirates. During this time it acted as a base for raids by the forces of Menteşe into the Aegean. In 1305 AD it was taken by Sasan (who had defected from Menteşe) but in 1340 AD it was taken by the emirate of Aydın. When the emirate of Aydın gained control of part of the western coast of Asia Minor it was able to develop maritime supremacy, used for piracy and to levy tribute. Menteşe was briefly restored to power by Timur, during which time İlyas Bey Mosque was built. The Ottomans conquered the city in 1425 AD.