The darkest era of Clan Lamont was undoubtedly during the mid 17th century. The brutal Covenanter wars and the Wars of the Three Kingdoms tore Scotland apart. Clan Lamont’s participation in these wars began with their alliance with the Campbells but ended in what is now known as the Dunoon Massacre. The chief of the clan during this time was Sir James Lamont of that Ilk. In 1634, Sir James represented the Barons of Argyll in Parliament. With the start of the following Wars of the Three Kingdoms, Lamont was sent a charter by King Charles I to crush the rebels. Even though the Lamont chief was a Royalist sympathizer and wished to obey Charles, he had no choice but to join forces with the more powerful Marquess of Argyll, who was also his brother in law. After the Covenanter loss at the Battle of Inverlochy, Sir James was released by the Royalist victors and was able to side with the Marquess of Montrose and actively support the Royalist cause. Lamont then joined forces with Alasdair MacColla and invaded the lands of the Campbells. Sir James’ brother, Archibald, led a force of Lamonts across Loch Long and, together with MacColla’s Irish contingent, landed at the Point of Strone. Their force then laid waste to large areas under Campbell control. The Lamonts were particularly brutal in North Cowal, and singled out Dunoon. During the destruction their forces wrought on the Campbells, MacColla’s men including Lamont clans men committed many atrocities. Sir James Lamont ravaged the lands of Strachur, killing thirty-three men, women and children. His force destroyed much grain and drove off 340 cattle and horses.

Several months later in May 1646, while the Lamonts were home at the castles of Toward and Ascog, they were besieged by Campbell forces seeking revenge. By 1 June 1646 the Campbells brought cannon forward to shell the Lamont strongholds. Two days later Sir James Lamont, in a written agreement of quarter and liberty for himself and his followers, surrendered and persuaded the other garrison at Ascog Castle to likewise lay down arms and surrender to the Campbells. Although the Campbells had agreed to the Lamonts terms of surrender, they immediately took the surrendered garrisons to Dunoon by boat. The Lamont strongholds were then looted and burnt to the ground. Sir James and his closest kin were shipped to Inveraray Castle, although he was held in the dungeons of Dunstaffnage Castle for the next five years. At Inverary, Sir James was forced to sign over all of the Lamont lands to Clan Campbell. In the churchyard at Dunoon, about a hundred Lamonts were sentenced to death and executed. Thirty-six of the clan’s high-ranking gentlemen were hanged from a tree in the churchyard, cut down and then buried either dead or alive in a common grave. After languishing in captivity for years, Sir James Lamont was brought to Stirling Castle in 1651 to answer for his actions with Alasdair MacColla for their devastations in Argyll. Lamont was eventually spared trial though, when King Charles II led his ill-fated Scots forces into England to be later defeated at the Battle of Worcester. Lamont was finally released when the forces of Oliver Cromwell took Stirling. Cromwell’s triumph also invalidated the “contract” that Sir James was forced to sign in captivity, and Clan Lamont regained its lands. It has been reputed that the total damage inflicted by the Campbells upon the Lamont estates was in excess of £600,000 Scots (£50,000 sterling). Argyll himself was able to recover £2,900 Scots (almost £245 sterling) for the entertainment and lodging of the Lamont chief while in captivity.

In 1661, the ringleader of the Dunoon Massacre, Sir Colin Campbell, was brought to justice. He stood trial on charges of High Treason, was found guilty, and then beheaded. A popular story is that the written terms of the surrender at Toward had survived by being hidden in the hair of the sister of James Lamont and its production at the trial sealed the Campbell’s fate.