The name Macquarrie derives from the Gaelic personal name, Guaire, meaning "noble" or "proud". According to tradition, Guaire was the brother of Finagon from whom the Mackinnon chiefs descend. This small clan possessed the little island of Ulva lying opposite the west coast of Mull, a small portion of Mull itself and Staffa, famous for "Fingal's Cave", but despite their size they were an ancient clan recorded as members on the councils of the Lord of Isles.

It is said that a former chief of the clan, Cormac Mor supported King Alexander II in his campaign in Argyll in 1249 and that Hector Macquarrie of Ulva fought with Robert the Bruce at Bannockburn. However the first authentic recording of a a Macquarrie of Ulva is in 1463, witnessing a charter of the Lord of the Isles. In 1609 the Macquarrie chief was one of the Highland chiefs kidnapped by James VI and compelled to sign the Statutes of Iona. After the forfeiture of the Lordship of the Isles the Macquarries followed the Macleans of Duart, who then dominated Mull. Due to this alliance the Macquarries suffered severly at Inverkeithing in 1651 when their chief, Allan and many of their clansmen died alongside the Macleans fighting for Charles II.

Lachlan Macquarrie of Ulva the 16th and last chief, who entertained Dr. Johnson and Boswell in 1773 was forced to sell his lands in 1778. He died in Mull in 1818 at the age of 103, leaving the chiefship dormant. The most famous member of the clan was Lachlan Macquarrie cousin to the last chief who became Governor of New South Wales after Captain Bligh was dismissed. Under his guidance the colony prospered and the foundations of Sydney were begun.