While the O'Dwyers are strongly associated with south Leinster (the most easterly of Ireland's four provinces), it is beyond doubt that the main territory under their control was an ancient district called Kilnamanagh in County Tipperary, Ireland. The name still survives as a modern civil barony, and extends over perhaps 100 sq. miles in the mountains between Limerick, Tipperary, Cashel and Thurles. The crumbling ruins of nine of the O'Dwyer castles can still be seen on the Kilnamanagh landscape even today.

The territory of Kilnamanagh was lost to the clan in the aftermath of the Cromwellian wars of the mid-seventeenth century, following the ill-fated capture of Cashel, the ancient Celtic seat of the Munster kings, by Philip O'Dwyer, the last clan chief. The clan was scattered - a few were permitted to take up lands west of the River Shannon in County Clare and other places, but the majority were part of the estimated 7,000 Irish who were exiled to mainland Europe with Colonel Edmund O'Dwyer, the leader of the Munster forces who surrendered to the Cromwellian army at Cahir, Co. Tipperary in 1652. Doubtless, many of their descendants are to be found across Europe today, though the surname has probably been modified to suit local pronunciation. For example in France, it appears as 'Haudoire'. It is interesting to note that many O'Dwyers remained or returned to their ancient territory of Kilnamanagh, because, even today, the highest concentration of the surname in the world is still to be found in this corner of Tipperary.