In the south, Greece was divided among a number of competing political units. After 1204 the dukes of Athens (mostly of French or Italian origin) controlled much of central Greece, with their main base at Thebes. They had political interests to the north and in the Peloponnese. However, in 1311 the Catalan Grand Company established its power over the duchies of Athens and Thebes, turning out their Latin lords. Under the protection of the Aragonese king Frederick II of Sicily (three sons of whom became dukes of Athens), they dominated the region until the Navarrese Company (an army of mercenaries originally hired by Luis of Evreux, brother of Charles II of Navarre, to help assert his claim over Albania and then temporarily in the service of the Hospitallers, a military-monastic order) took Thebes in 1378 or 1379. This weakened Catalan power and opened the way for the Florentine Acciajuoli, lords of Corinth, to take Athens in 1388. The latter then ruled all three regions until their defeat at the hands of the Ottomans in the 1450s.

The Peloponnese

In the Peloponnese the political rivalry between the Byzantines and the Frankish principality of Achaea dominated. The principality was at its most successful under its prince William II Villehardouin (1246–78), but in 1259 he had to cede a number of fortresses, including Mistra, Monemvasiá, and Maina, to the Byzantines. Internecine squabbles weakened resistance to Byzantine pressure, especially from the 1370s onward, when Jacques de Baux hired the Navarrese Company to fight for his claim to the principality. Upon his death in 1383, the Navarrese exercised effective political control over the Frankish territories under the commanders of the company. The last Navarrese prince, Pierre de Saint-Superan, joined the Ottomans in 1401 to raid Byzantine possessions in the southern Peloponnese; he died in 1402. He was succeeded by his widow, Maria Zaccaria, representative of an important Genoese merchant and naval family. She passed the title to her nephew Centurione II Zaccaria, who lost much of the territory to the Byzantine despotate of the Morea. In 1430 he married his daughter to the Byzantine despotēs Thomas Palaeologus, handing over his remaining lands as her dowry. From that time on, the Byzantine despotate of the Morea effectively controlled most of the Peloponnese. However, the Ottoman presence and the fall of Constantinople to Sultan Mehmed II in 1453 effectively ended that final period of Byzantine rule. The Morea resisted Ottoman conquest until 1460, when it was finally incorporated into the Ottoman Empire (a year earlier than the empire of Trebizond, which fell in 1461). All of Greece was by that time under Ottoman authority, with the exception of some of the islands, which retained a tenuous independence under Venetian or Genoese protection.

Serbian and Ottoman advances

Byzantine power in the northern Greek regions was effectively destroyed by the expansion of the Serbian empire under Stefan Dušan, the results of which included the loss of Epirus, Thessaly, and eastern Macedonia. From the 1350s the Ottomans established themselves in Europe, taking the chief towns of Thrace in the 1360s and Thessalonica in 1387. Apart from the despotate of the Morea, therefore, and certain of the Aegean isles, there remained in Greece no Byzantine imperial possessions by the beginning of the 15th century.

The islands

A particularly complex picture is represented by the islands, which were a focus for the activities of the Seljuqs and later the Ottomans, the Venetians and Genoese, and the Byzantines. Following the Fourth Crusade, much of the southern part of the Aegean came under Venetian authority, and, although Byzantine power was restored for a while in the late 13th century, Náxos (Náchos) remained the centre of the Latin duchy of the Archipelago, established in 1207 among the Cyclades by Marco Sanudo, a relative of the Venetian doge, or magistrate, with a body of plundering merchants and nobles. Initially under the overlordship of the Latin emperor at Constantinople, the duchy later transferred its allegiance to Achaea in 1261 and to Naples in 1267, although Venice also claimed suzerainty. The Sanudo family was replaced in 1383 by the Lombard Crispi family, which retained its independence until 1566. At that time the duchy was conquered by the Ottomans, although it was ruled by an appointee of the sultan until 1579, when it was properly incorporated into the state.

The remaining islands were held at different times by the Venetians, the Genoese, the Hospitallers, and the Turks. Rhodes played a particular role in the history of the Hospitallers’ opposition to the Ottomans. Until the early 13th century the island had been in the hands of a succession of Italian adventurers, most of whom acknowledged the overlordship of the emperor at Nicaea. In 1308 the Hospitallers took control, having been based on Cyprus since 1291, the time of their expulsion from the Holy Land. Rhodes fell in 1523, when the Hospitallers were permitted to remove to Malta. Of the northern Aegean islands, Lemnos remained Byzantine until 1453 before coming for a while under the rule of the Gattilusi of Lésbos, whose independence of the Ottomans ended in 1462. In 1460 it was awarded to Demetrius Palaeologus, formerly despotēs of the Morea, along with the island of Thasos (the latter having come under Ottoman domination in 1455). In 1479 it was occupied by Ottoman forces and officially incorporated into the Ottoman state. Other islands had equally checkered histories. Náxos and Chíos (Khíos) fell in 1566, although complete Ottoman control was not achieved until 1715, when Tenedos, which remained under Venetian control until that year, was taken.

The real exception to the Ottoman success in the Aegean, however, was Crete. Separately administered until the 820s, when it was seized by Spanish Arabs, it was conquered in 961 by the general and later Byzantine emperor Nicephoros II Phocas. After 1204 it was handed over to Boniface of Montferrat, who proceeded to sell it to Venice. Although oppressive and unpopular, Venetian rule witnessed the evolution of a flourishing Italo-Hellenic literary and political culture. After a long siege of Candia (now Irákleio) and the creation and collapse of temporary alliances between Venice and various Western powers on the one hand and the Ottomans and their supporters on the other, the island passed into Ottoman hands in 1669.