The words for two different parts of a castle come from the same source. The word dungeon, meaning “a dark usually underground prison,” comes from the French word donjon, which also gives us our English word donjon, meaning “an inner tower in a castle.” Dungeon was first used in English in the 14th century for the strong tower in the inner part of the castle. Defenders could retreat to this tower if attackers got inside the castle walls. Part of the tower usually included an underground room, the dungeon, usually used for prisoners. Throughout its history, the word dungeon has had many spellings. Sometimes it was spelled donjon like the French word it comes from, and sometimes in other ways. In time the spelling donjon came to be used mostly for the castle tower, and the spelling dungeon mostly for the underground room or prison.
The king threw them in the dungeon.
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Middle English dongeon, donjon, from Anglo-French donjun, from Vulgar Latin *domnion-, domnio keep, mastery, from Latin dominus lord — more at dominate