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During the reign of Saint Gebre Mesqel Lalibela (a member of the Zagwe Dynasty, who ruled Ethiopia in the late 12th century and early 13th century) the current town of Lalibela was known as Roha. The saintly king was given this name due to a swarm of bees said to have surrounded him at his birth, which his mother took as a sign of his future reign as Emperor of Ethiopia. The names of several places in the modern town and the general layout of the rock-cut churches themselves are said to mimic names and patterns observed by Lalibela during the time he spent in Jerusalem and the Holy Land as a youth.

Lalibela is said to have seen Jerusalem and then attempted to build a new Jerusalem as his capital in response to the capture of old Jerusalem by Muslims in 1187. As such, many features have Biblical names – even the town's river is known as the River Jordan. It remained the capital of Ethiopia from the late 12th century and into the 13th century.

The first European to see these churches was the Portuguese explorer Pêro da Covilhã (1460–1526). Portuguese priest Francisco Álvares (1465–1540), who accompanied the Portuguese Ambassador on his visit to Lebna Dengel in the 1520s.