The MacDonald clan, which was spread over north-western Scotland and north-eastern Ireland, sided with the Royalists and Irish Confederates. Their deadly enemies, the Clan Campbell, sided with the Scottish Covenanters. In 1642 men from Islay were fighting in Ireland with the Covenanters, the cause favoured by the Campbells, but also with the native Irish who supported King Charles I.
Early in the war, Alasdair MacColla was forced to flee the Western Isles, which were attacked by a Covenanter/Campbell force. Colla, his father was taken prisoner by the Campbells. MacColla, who was a Catholic, quickly became involved in fighting the Protestant settlers there. In 1642, the Scottish Covenanters landed an army in Ulster and drove the Irish Catholic forces out of the province. In 1644, he was selected by the Supreme Council of Confederate Ireland to lead an expedition to Scotland to aid the Royalists there against the Covenanters. In the subsequent Scottish Civil War, MacColla and Montrose won a series of victories at Tippermuir, Aberdeen, Inverlochy, Auldearn, Alford and Kilsyth. MacColla also took the opportunity to pillage the Campbell lands, killing all the men he could find there. However, he and Montrose parted company because MacColla's priorities lay in the western Highlands, whereas Montrose wanted to secure the Lowlands and ultimately England for the Royalist cause. As a result, both of them were defeated separately by the Covenanters in 1646.
MacColla's men committed a series of atrocities against the civilians of clan Campbell. During his two periods in occupation of Argyle, the Campbell territory (1645 and 1647), MacColla had all men of military age killed, whether they were in arms or not. On one infamous occasion, MacColla had a whole barn full of Campbells (including women and children) burned, in an incident known as the "Barn of Bones".
MacColla's father, who was a prisoner of the Campbells, was killed in retaliation for his son's atrocities in the Campbell country. MacColla himself retreated to Kintyre and then to Ireland, where he re-joined the Irish Confederates in 1647. His troops, (both Irish survivors of the 1644 expedition and Scottish Highlanders) were split up and assigned to the Leinster and Munster armies, with MacColla attached to the latter. MacColla's men were mostly killed in the Confederate defeats at the battle of Dungans Hill in Meath and then at the battle of Knocknanauss in Cork.
Alasdair MacColla himself was killed by English Parliamentarian soldiers at Knocknanauss after he had been taken prisoner a century after Shane Ó Neill, rejecting overtures from Thomas Radclyffe, 3rd Earl of Sussex, the lord deputy from 1556, Shane refused to help the English against the Scottish settlers on the coast of Antrim, allying himself instead with the MacDonnells, the most powerful of these immigrants. Sussex, indignant at Shane's request for his sister's hand in marriage, and his demand for the withdrawal of the English garrison from Armagh, received no support from the Queen, who sent the earl of Kildare to arrange terms with Ó Neill. O'Neill turned his hand against the MacDonnells, claiming that he was serving the Queen of England in harrying the Scots. He fought an indecisive battle with Sorley Boy MacDonnell near Coleraine in 1564, and the following year marched from Antrim through the mountains by Clogh to the neighbourhood of Ballycastle, where he routed the MacDonnells at the Battle of Glentasie and took Sorley Boy prisoner.The importation of galloglas into Ireland was a major factor in containing the Anglo-Norman invasion of the 12th century, as their ranks stiffened the resistance of the Irish lordships. Galloglas fighters were joined by native Irish mercenaries called buanadha (literally "quartered men") and by newer Scottish mercenaries known as "redshanks".
The flow of mercenaries into Ireland was such a threat to English occupation that Queen Elizabeth I took steps against them in 1571 - around 700 of them were executed after the first of the Desmond Rebellions. In spite of the increased use of firearms in Irish warfare, galloglas remained an important part of Hugh Ó Neill's (Shane Ó Neill's rival) forces in the Nine Years War (Ireland). After Hugh's inauguration as the Ó Neill on Turlough's resignation as tanist in 1595, he was left without a rival in the north. The Northern Uí Néill ruled much of what is now Ulster. Their kinsmen, the Southern Uí Néill, were Kings of Brega (Meath). The kingship of Leinster was held by the dynamic Ui Cheinnselaigh dynasty. The first Norman knight to land in Ireland was Richard fitz Godbert de Roche in 1167, but it was not until 1169 that the main forces of Normans, Welsh and Flemings landed in Wexford. In Dublin, he proceeded with Mountjoy, Hugh Ó Neill heard of the accession of King James, at whose court he presented himself in June accompanied by Rory O'Donnell, who had become chief of the O'Donnells after the departure of his brother Hugh Roe. After the combined Irish defeat at the Battle of Kinsale in 1601, recruitment of galloglas waned, although Scottish Highland mercenaries continued to come to Ireland until the 1640s (notably Alasdair MacColla).
In the great civil war the Clanranald of Lochaber were very active on the king's side. Soon after the Restoration, Alexander Macdonald Glas, the young chief of Keppoch, and his brother were murdered by some of their own discontented followers. Coll Macdonald was the next chief. Previous to the Revolution of 1688, the feud between his clan and the Mackintoshes, regarding the lands he occupied, led to the last clan battle that was ever fought in the Highlands. The Mackintoshes having invaded Lochaber, were defeated on a height called Mulroy. So violent had been Keppoch's armed proceedings before this event that the government had issued a commission of fire and sword against him. After the defeat of the Mackintoshes, he advanced to Inverness, to wreak his vengeance on the inhabitants of that town for supporting the former against him, if they did not purchase his forbearance by paying a large sum as a fine. Dundee, however, anxious to secure the friendship of the people of Inverness, granted Keppoch his own bond in behalf of the town, obliging himself to see Keppoch paid 2000 dollars, as a compensation for the losses and injuries he alleged he had sustained from the Mackintoshes. Keppoch brought to the aid of Dundee 1000 Highlanders and as Mackintosh refused to attend a friendly interview solicited by Dundee, Keppoch, at the desire of the latter, drove away his cattle. We are told that Dundee " used to call him Coll of the cowes, because he found them out when they were driven to the hills out of the way." He fought at the battle of Killiecrankie, and, on the breaking out of the rebellion of 1715, he joined the Earl of Mar, with whom he fought at Sheriffmuir. His son, Alexander Macdonald of Keppoch, on the arrival of Prince Charles in Scotland in 1745, at once declared for him, and at a meeting of the chiefs to consult as to the course they should pursue, he gave it as his opinion that as the prince had risked his person, and generously thrown himself into the hands of his friends, they were bound, in duty at least, to raise men instantly for the protection of his person, whatever might be the consequences.
During the Civil War the MacDonalds of Clan Ranald supported the Royalist cause and distinguished themselves when they served under James Graham the 1st Marquess of Montrose. The MacDonalds of Clan Ranald were led by their chief who was just 14 years of age led 500 men of the clan at the Battle of Killiecrankie in 1689. The MacDonalds always supported the House of Stewart and the Jacobite cause. The MacDonalds of Clan Ranald fought at the Battle of Sheriffmuir in during the initial early risings of 1715. In the later Jacobite uprisings of 1745 to 1746 the MacDonalds of Clan Ranald were amongst the Macdonalds who fought on the honoured right wing at the Battle of Prestonpans and the Battle of Falkirk (1746). However at the Battle of Culloden the three Macdonald regiments of Clan Ranald, Clan MacDonnell of Glengarry, and the Clan MacDonald of Keppoch formed the left wing. The seat of the Clan MacDonald of Clan Ranald chief was at Castle Tioram.
Septs of Clan MacDonald of Clan Ranald include the following. Other branches of Clan Macdonald have different septs. Allan, Allanson, Currie, MacAllan, MacBurie, MacEachin, MacGeachie, MacGeachin, MacIsaac, MacKeachan, Mackechnie, MacKeochan, MacKessack, MacKessock, MacKichan, MacKissock, MacMurrich, MacVarish, MacVurrich, MacVurie.