John Munro, 2nd of Lemlair (fl. mid 17th century) was a Scottish soldier who fought as a Colonel in the Wars of the Three Kingdoms. His seat was at Lemlair House.
John Munro, 2nd of Lemlair was the eldest son of Andrew Munro, 1st of Lemlair who was in turn the fifth son of Robert Mor Munro, 15th Baron of Foulis, chief of the Clan Munro.
John Munro, 2nd of Lemlair entered into a military career and rose to the rank of Colonel, taking a prominent part in the wars involving James Graham, 1st Marquess of Montrose from 1639 to 1649.
John Munro was a member of the assize at the Tollbooth of Inverness on 4 June 1616 when John Gordon, 14th Earl of Sutherland was served heir to his father. In 1617 John Munro was amongst those chosen to help settle a dispute between the same Earl of Sutherland and Donald Mackay, 1st Lord Reay over the boundaries of their estates.
In May 1639 John Munro, 2nd of Lemlair commanded a division of the 4000 strong Covenanter army. They went to Morayshire with the intention of opposing the advance of the Royalists to the North Highlands. They encamped at Speyside to keep the Clan Gordon and their allies from entering into Moray, remaining there until pacification was signed on 20 June. Soon afterwards John Munro of Lemlair, following the example of James Graham, 1st Marquess of Montrose severed his connection with the Covenanters and joined the Royalists.
On 22 February 1649, John Munro of Lemlair along with Hugh Fraser, Thomas Mackenzie of Pluscardine and Sir Thomas Urquhart of Cromarty led a royalist rising in connection with plans for the Marquess of Montrose to reattempt to recover the kingdom. Now known as the Siege of Inverness (1649) they entered the town of Inverness, expelled the troops from the garrison and demolished the walls and fortifications. A Council of War was held on 26 February in which Munro was one of the members. Upon the approach of General David Leslie, Lord Newark, the Royalists retreated back into Ross-shire. Leslie managed to negotiate peaceful terms with Munro, Fraser and Urquhart but not with Mackenzie.