Margariti began as a military installation. An Ottoman fort rose here in the first half of the 16th century, its garrison drawn from the Albanian Mazreku tribe whose tax revenues funded the soldiers' pay. By 1551, the surrounding district had been renamed for the settlement. The frontier position — pressing up against Venetian-held Parga along the Ionian coast — guaranteed both strategic importance and constant friction.

The Venetians struck hard in the 16th century. A force of six thousand Venetians and Corfiots under commander Sebastiano Venier besieged the fort for four days, seized it, and burned it to the ground. Venice considered the event significant enough to commission a painting for the Doge's Palace to commemorate the destruction. But the town rebuilt. By 1670, when the Ottoman traveller Evliya Çelebi passed through, Margariti had grown into a place of five to six thousand people, split into seven neighborhoods, with two Friday mosques bearing stone minarets, seven neighborhood prayer rooms, two schools, a hamam, two caravanserais, and a madrasa under construction. It was, by the measure of its era, a substantial and self-sufficient Epirot town.

Through the 18th and 19th centuries Margariti remained a center of Muslim Albanian life in the region the Albanians called Chameria — the coastal strip running through what is now northwestern Greece. In 1880, Muslim Albanians made up 82 percent of the town's population, with a total of around 1,100 inhabitants. The surrounding Kaza was 80 percent Muslim. The Albanian writer Sami Frashëri described Margariti around 1898 as a town of some three thousand Muslim Albanian residents.

When the Balkan Wars reshaped the map of the southern Balkans, the Greek army took Margariti in February 1913, and the town was formally incorporated into Greece under the Treaty of London in May of that year. The change was not welcome. Village elders gathered and declared their resistance to incorporation. In the years that followed, the town's Muslim Albanian population declined significantly: from roughly 2,600 in 1913 to about 1,800 by 1920. By the 1928 census, of 1,805 inhabitants, only around 200 were recorded as ethnically Greek — the gradual Hellenization of the area had begun, but Margariti was still recognizably a Cham Albanian town. It also held Jakup Veseli, a representative of Chameria at the 1912 Vlora Congress who had signed the Albanian Declaration of Independence, and Hamdi Çami, the region's Albanian deputy in the Ottoman Parliament — figures who embodied the community's deep roots in the territory.

The Second World War brought Margariti into some of the most contested and violent episodes of the Greek occupation years. Italian Fascist troops occupied the town beginning in 1941. Armed Cham Albanian groups committed massacres and lootings against the surrounding population during the occupation — actions that are part of the documented record and that sharply deepened the antagonisms of those years. Cham monuments in Margariti were largely destroyed during the war.

At the war's end, in 1944–45, ELAS forces expelled the Cham Albanian community from Margariti and the surrounding region. Those who could escape fled across the border to Albania. The mosques, tekkes, and other buildings that had defined the Islamic character of the town for four centuries were torn down, blown up, or burned. The town that had once housed five to six thousand people in seven neighborhoods was largely deserted.

The Cham Albanian question — the expulsion of a community that had lived in this region for centuries — remains historically and politically contested between Greece and Albania. What is not in dispute is the human reality: real families lost their homes, their graves, and their connection to a landscape they had inhabited for generations. The material culture of four hundred years of Muslim Albanian life in Margariti was, in the space of a few months, erased from the ground.

Today Margariti is a quiet village, its population counted at 1,931 in the 2021 census, part of the wider municipality of Igoumenitsa since the 2011 administrative reform. The Ottoman fort that started it all is gone. The mosques are gone. The hamam, the caravanserais, the tekkes — most vanished in the destruction of 1944–45 or the decades that followed.

What persists is the landscape itself: the rolling hills of Thesprotia, the olive groves, the hazy Ionian light that travelers have described across the centuries. Researchers from universities in Greece, Albania, and Croatia have worked to reconstruct Margariti's history from Ottoman defters, Venetian correspondence, and census records. A 2022 scholarly volume examined the town's emergence, development, and disappearance as a Muslim settlement at the far edge of the Islamic world. The people who once filled those seven neighborhoods are gone. The record of their lives is not.