In form at least the surname is Scottish, deriving from the place of the name in Annandale in Dumfriesshire, which was originally ‘Johns town’.

The original John was a Norman landowner in the area in the twelfth century, and instead of taking on the straightforward patronymic ‘Johnson’, his descendants adopted the placename as their surname, becoming Johnston(e)s.

This family, the source of virtually all Scottish bearers of the name, became one on the strongest and most unruly of the Border clans, and their long feud with another clan, the Maxwells, was notorious for its ferocity.

When the clans were eventually ‘pacified’ and scattered by James II, many Johnstons fled to Ulster where, like large numbers from the other clans - Elliots, Armstrongs, Nixons and others - they settled mainly in Co Fermanagh, where the surname is today the second most numerous in the county.

As well as these Johnstons, however, many others whose name was originally Johnson adopted the Scottish name. Such adoptions occurred predominantly in Ulster, and affected those of Scottish and of native Irish origin, with the Maclans of Caithness translating their surname as Johnson, and then altering it to Johnston in many cases, and the MacShanes of the Armagh/Tyrone district, a branch of the O’Neills, doing likewise. During Anglicization many Mc Keowns in Ireland had their name changed to Johnston. Mac Eoin in the Irish language translates to 'son of John'.

Courtesy of:
Edward MacLysaght's "Surnames of Ireland"