The Flanagans, as well as, the O'Flanagans are descendants of a number of Ó Flannagáin septs, to be found at different regions of the country.

The chief septs, were to be found in Counties Roscommon, Fermanagh, Monaghan and Offaly.  In Connacht, they were a part of the royal O Connors and were located near Elphin, in Co. Roscommon, and they were hereditary stewards to the Kings of Connacht.  The name is derived from Flann, which means 'red or ruddy'.

Today the name is ranked as the sixty ninth most numerous name in Ireland, with the greatest numbers found in the homelands, as well as Mayo and Galway.

Variants:  O'Flanagan, Flanaghan, Flannigan
From:  Heraldy Names, Ltd. Ballina, Ireland

(O) FLANAGAN  This surname is practically the same in both its Irish and anglicized forms, being in the former Ó Flannagáin, which is probably derived from the adjective flann meaning reddish or ruddy.  It belongs to Connacht both by origin and location (i.e. present distribution of population).  Flanagan, with of course O'Flanagan, for this is one of those names with which the prefix is frequently retained, is numbered among the hundred most commonest surnames in Ireland and has the sixty-ninth place on that list.  The greatest number of these are found in Co. Roscommon and in the counties of the western seaboard -- Mayo, Galway and Clare.  They sprang from one Flanagan, who was the same stock as the royal O'Connors and his line held the hereditary post of steward to the Kings of Connacht.  These, who were seated between Mantua and Elphin, represent the main O'Flanagan sept.  There were also minor septs and the same name in other parts of the country which were still represented in the seventeenth century; of Toorah in north-west Fermanagh and again of the barony of Ballybrit in Offaly.  Some descendants of these are still to be found in both these areas.

Donough O'Flanagan (b 1308), Bishop of Elphin, was famous abroad as well as at home for his hospitality and devotion.  Other notable Irishmen of the name were Roderick Flanagan (1828-1861), founder of the Sydney Chronicle; Thomas Flanagan (1814-1865), author of the History of the Church of England; and James Roderick Flanagan (1814-1900), voluminous author on Irish subjects.  Theophilus O'Flanagan (1760-1818), was a leading figure in the early Gaelic revival movement.
From Edward MacLysaght's, Irish Families, Their Names, Arms & Origins