On the 15th of April, 1569, Colin, along with Alexander Ross of Balnagown, Lachlan Mackintosh of Mackintosh, Walter Urquhart of Cromarty, Robert Munro of Fowlis, Hugh Rose of Kilravock, and several others, signed a bond of allegiance to James VI. and to James Earl of Murray as Regent. On the 21st of June, in the same year, before the Lord Regent and the Privy Council, Colin promised and obliged himself to cause Torquil Macleod of Lewis to obtain sufficient letters of slams from the master, wife, bairns, and principal kin and friends of the umquhile John Mac Ian Mhoir, and on the said letters of slams being obtained Robert Munro of Fowlis promised and obliged himself to deliver to the said Torquil or Colin the sum of two hundred merks consigned in Robert Munro's hands by certain merchants in Edinburgh for the assithment of slaughters committed at Lochcarron in connection with the fishings in that Loch. On the 1st of August, 1569, Colin signs a decree arbitral between himself and Donald Gormeson Macdonald, sixth of Sleat, the full text of which will be found at pp. 185-88 of Mackenzie's "History of the Macdonalds and Lords of the Isles."

In 1570 a quarrel broke out between the Mackenzies and the Munros. Leslie, the celebrated Bishop of Ross, who had been secretary to Queen Mary, dreading the effect of public feeling against prelacy in the North, and against himself personally, made over to his cousin Leslie of Balquhair, his rights and titles to the Chanonry of Ross, together with the castle lands, in order to divest them of the character of church property, and so save them to his family but notwithstanding this grant, the Regent Murray gave the custody of the castle to Andrew Munro of Milntown, a rigid presbyterian, and in high favour with Murray, who promised Leslie some of the lands of the barony of Fintry in Buchan as an equivalent but the Regent died before this arrangement was carried out - before Munro obtained titles to the castle and castle lands as he expected. Yet he ultimately obtained permission from the Earl of Lennox, during his regency, and afterwards from the Earl of Mar, his successor in that office, to get possession of the castle.

The Mackenzies were by no means pleased to see the Munros occupying the stronghold; and, desirous to obtain possession of it themselves, they purchased Leslie's right, by virtue of which they demanded delivery of the castle. This was at once refused by the Munros. Kintail raised his vassals, and, joined by a detachment of the Mackintoshes, [In the year 1573, Lachlan More, Laird of Mackintosh, favouring Kintail, his brother-in law, required all the people of Strathnairn to join him against the Munros. Colin, Lord of Lorn had at the time the adminstration of that lordship as the jointure lands of his wife, the Countesa Dowager of Murray, and he wrote to Hugh Rose of Kilravock: "My Baillie off Strathnarne, for as much as it is reported to me that Mackintosh has charged all my tenants west of the water of Naim to pass forward with him to Ross to enter into this troublous action with Mackenzie against the Laird of Fowlis, and because I will not that any of mine enter presently this matter whose service appertains to me, wherefore I will desire you to make my will known to my tenants at Strathnarne within your Bailliary, that none of them take upon hand to rise at this present with Mackintosh to pass to Ross, or at any time hereafter without my special command and goodwill obtained under such pains," etc. (Dated) Darnoway, 28th of June, 1573. - "Kilravock Writs," p.263.] garrisoned the steeple of the Cathedral Church, and laid siege to Irvine's Tower and the Palace. The Munros held out for three years, but one day the garrison becoming short of provisions, they attempted a sortie to the Ness of Fortrose, where there was at the time a salmon stell, the contents of which they attempted to secure. They were commanded by John Munro, grandson of George, fourth laird of Fowlis, who was killed at the battle of "Bealach-nam-Brog." They, were immediately discovered, and quickly followed by the Mackenzies, under lain Dubh Mac Ruairidh Mhic Alastair, who fell upon the starving Munros, and, after a desperate struggle, killed twenty-six of their number, among whom was their commander, while the victors only sustained a loss of two men killed and three or four wounded. The remaining defenders of the castle immediately capitulated, and it was taken possession of by the Mackenzies. Subsequently it was confirmed to the Baron of Kintail by King James VI. [Sir Robert Gordon, p. 154, and MS. Histories of the Family.] Roderick Mor Mackenzie of Redcastle seems to have been the leading spirit in this affair. The following document, dated at Holyrood House, the 12th of September 1573, referring to the matter will prove interesting -

Anent our Sovereign Lord's letters raised at the instance of Master George Munro, making mention: that whereas he is lawfully provided to the Chancellory of Ross by his Highness's presentation, admission to the Kirk, and the Lords' decree thereupon, and has obtained letters in all the four forms thereupon and therewith has caused charge the tenants and intromitters with the teind sheaves thereof, to make him and his factors payment; and in the meantime Rory Mackenzie, brother to Colin Mackenzie of Kintail, having continual residence in the steeple of the Chanonry of Ross, which he caused to be built not only to oppress the country with masterful theft, sorning, and daily oppression, but also for suppressing of the word of God which was always preached in the said Kirk preceding his entry thereto, which is now become a filthy stye and den of thieves; has masterfully and violently with a great force of oppression, come to the tenants indebted in payment of the said Mr George's benefice aforesaid and has masterfully reft them of all and whole the fruits thereof; and so he having no other refuge for obtaining of the said benefice, was compelled to denounce the said whole tenants rebels and put them to the horn, as the said letters and execution thereof more fully purports; and further is compelled for fear of the said Mr George's life to remain from his vocation whereunto God has called him. And anent the charge given to the said Rory Mackenzie to desist and cease from all intromitting, uptaking, molesting or troubling of the said Mr George's tenants of his benefice above-written for any fruits or duties thereof, otherwise than is ordered by law, or else to have compeared before my Lord Regent's grace and Lords of Secret Council at a certain day bypast, and show a reasonable cause why the same should not be done; under the pain of rebellion and putting him to the horn, with certification to him, and he failing, letters would be directed simpliciter to put him to the horn, like as is at more length contained in the said letters, execution and endorsement thereof. Which being called, the said Master George compeared personally, and the said Rory Mackenzie oftimes called and not compearing, my Lord Regent's grace, with advise of the Lords of Secret Council, ordained letters to be directed to officers of arms, Sheriffs in that part, to denounce the said Rory Mackenzie our Sovereign Lord's rebel and put him to the horn and to escheat and bring in all his moveable goods to his Highness's use for his contempt. [Records of the Privy Council.]

In December of the same year Colin has to provide cautioners, for things laid to his charge, to the amount of ten thousand pounds, that he shall remain within four miles of Edinburgh, and eastward as far as the town of Dunbar, and that he shall appear before the Council on a notice of forty-eight hours. On the 6th of February following other cautioners bind themselves to enter him in Edinburgh on the 20th of May, 1574, remaining there until relieved, under a penalty of ten thousand pounds. He is entered to keep ward in Edinburgh on the 1st March, 1575, and is bound to appear before the Council when required under a similar penalty. On the 10th of April following he signs a bond that Alexander Ross shall appear before the Lords when required to do so. On the 25th of May, 1575, at Chanonry, Robert Munro of Fowlis and Walter Urquhart, Sheriff of Cromarty, bind themselves their heirs, and successors, under a penalty of five thousand pounds, that they shall on a month's notice enter and present Roderick Mor Mackenzie of Redcastle before the King and the Privy Council and that he shall remain while lawful entry be taken of him, and that he shall keep good rule in his country in the meantime. On the same day Colin, his brother, "of his own free motive will" binds himself and his heirs to relieve and keep these gentlemen scaithless of the amount of this obligation. He is one of several Highland chiefs charged by the Regent and the Privy Council on the 19th of February, 1577-78, to defend Donald Mac Angus of Glengarry from an expected invasion of his territories by sea and land. [Register of the Privy Council.]

The disturbed state of the country was such, in 1573, that the Earl of Sutherland petitioned to be served heir to his estates, at Aberdeen, as he could not get a jury together to sit at Inverness, "in consequence of the barons, such as Colin Mackenzie of Kintail, Hugh Lord Lovat, Lachlan Mackintosh of Dunachton, and Robert Munro of Fowlis, being at deadly feud among themselves." [Antiquarian Notes, p. 79]

In 1580 a desperate quarrel broke out between the Mackenzies and Macdonalds of Glengarry. The Chief of Glengarry inherited part of Lochalsh, Lochcarron, and Lochbroom, from his grandmother, Margaret, one of the sisters and co-heiresses of Sir Donald Macdonald of Lochalsh, and grand-daughter of Celestine of the Isles. Kenneth, during his father's life, had acquired the other part by purchase from Dingwall of Kildun, son of the other co-heiress of Sir Donald, on the 24th November, 1554, and Queen Mary confirmed the grant by Royal charter. Many causes leading to disputes and feuds can easily be imagined with such men in close proximity. Glengarry and his followers "sorned" on Mackenzie's tenants, not only in the immediate vicinity of his own property of Lochcarron, but also during their raids from Glengarry, on the outskirts of Kintail, and thus Mackenzie's dependants were continually harrassed by Glengarry's cruelty and ill-usage. His own tenants in Lochalsh and Lochcarron fared little better, particularly the Mathesons in the former, and the Clann Ian Uidhir in the latter, who were the original possessors of Glengarry's lands in that district. These tribes, finding themselves in such abject slavery, though they regularly paid their rents and other dues, and seeing how kindly Mackenzie used the neighbouring tenantry, envied their more comfortable state and "abhorred Glengarry's rascality, who would lie in their houses (yea, force their women and daughters) so long as there was any good to be given, which made them keep better amity and correspondence with Mackenzie and his tenants than with their own master and his followers. This may partly teach how superiors ought always to govern and oversee their tenantry and followers, especially in the Highlands, who were ordinarily made up of several clans, and will not readily underlie such slavery as the Incountry Commons will do."

The first serious outbreak between the Glengarry Macdonalds and the Mackenzies originated thus: One Duncan Mac Ian Uidhir Mhic Dhonnachaidh, known as "a very honest gentleman," who, in his early days, lived under Glengarry, and was a very good deerstalker and an excellent shot, often resorted to the forest of Glasletter, then the property of Mackenzie of Gairloch, where he killed many of the deer. Some time afterwards, Duncan was, in consequence of certain troubles in his own country, obliged to leave, and he, with all his family and goods, took up his quarters in Glen Affrick, close to the forest. Soon after, he went, accompanied by a friend, to the nearest hill, and began his favourite pursuit of deerstalking. Mackenzie's forester perceiving the stranger, and knowing him as an old poacher, cautiously walked up, came upon him unawares, and demanded that he should at once surrender himself and his arms. Duncan, finding that Gairloch's forester was only accompanied by one gillie, "thought it an irrecoverable affront that he and his man should so yield, and refused to do so on any terms, whereupon the forester being ill-set, and remembering former abuses in their passages," he and his companion killed the poachers, and buried them in the hill. Fionnla Dubh Mac Dhomh'uill Mhoir and Donald Mac Ian Leith, the latter a native of Gairloch, were suspected of the crime, but it was never proved against them, though they were both several times put on their trial by the barons of Kintail and Gairloch.

About two years after the murder was committed, Duncan's bones were discovered by one of his friends, who had continued all the time diligently to search for him. The Macdonalds always suspected foul play, and this having now been placed beyond question by the discovery of the bodies of the victims, a party of them started, determined to revenge the death of their clansman; and, arriving at Inchlochell, Glenstrathfarrar, then the property of Rory Mor Mackenzie of Redcastle, they found Duncan Mac Ian Mhic Dhomh'uill Mhoir, a brother of the suspected Finlay Dubh, without any fear of approaching danger, busily engaged ploughing his patch of land, and they at once attacked and killed him. The renowned Rory Mor, hearing of the murder of his tenant, at once despatched a messenger to Glengarry demanding redress and the punishment of the assassins, but Glengarry refused. Rory was, however, determined to have satisfaction, and he resolved, against the counsel of his friends, to have retribution for this and previous injuries at once and as best he could. Having thus decided, he at once sent for his friend, Dugall Mackenzie of Applecross, to consult him as to the best mode of procedure to ensure success.

Glengarry lived at the time in the Castle of Strone, Lochcarron, and, after consultation, the two Mackenzies resolved to use every means in their power to capture him, or some of his nearest relatives. For this purpose Dugall suggested a plan by which he thought he would induce the unsuspecting Glengarry to meet him on a certain day at Kishorn. Rory Mor, to avoid any suspicion, was to start at once for Lochbroom, under cloak of attending to his interests there; and if Macdonald agreed to meet Dugall at Kishorn, he would immediately send notice of the day to Rory. No sooner had Dugall arrived at home than, to carry out this plan, he dispatched a messenger to Glengarry informing him that he had matters of great importance to communicate to him, and that he wished, for that purpose, to meet him on any day which he might deem suitable.