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"This name has been closely associated with Kilkenny since 1550. The townland of Marnellsmeadows now forms part of that town. The family became hibernicized. The name was originally Warnell, a derivative of Warner."
Edward MacLysaght, "The Surnames of Ireland", (Dublin) 1973.

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So the family is of distant English origin. Warner can be from the old Norman personal name Warnier (French, Guarnier, Garnier), or from the occupational name Warrener, identifying a sort of gamekeeper, whose job was ensuring that rabbit warrens were well stocked as a source for food.