The name Zagori first appears in 1321, but the area was settled before, by Vlach shepherds and wealthy Byzantine families who had fled Constantinople after it was conquered by Crusaders in 1204. Under Ottoman rule, the region's leaders negotiated religious autonomy and tax exemptions. In the 18th century, Zagori men began to emigrate, building businesses in other countries. The wealth and worldly knowledge they sent back illuminated the villages; each had a large school, and full literacy. Benefactors also built an elaborate infrastructure of kalderimia (stone paths), mountain staircases and bridges linking the villages, so that it was said that Zagori folks never muddied their shoes.
As the last of the Ottoman tax deals were abolished in the 19th century, families began to leave the area for good. During WWII the Germans bombed many of the eastern Zagori villages, in retaliation for harbouring resistance fighters. In the 1950s, the villages were near empty, but Sarakatsani shepherd families that had previously migrated through the area, began to settle. Roads were improved in the 1970s, which helped open the area to visitors and the ecotourism business that flourishes today.