Sir James, twelfth of Innes was chief esquire to James the third and entertained James the fourth at Innes Castle in 1490. He and his son were noted patrons of the arts and often would host evenings of art for the Scottish gentry.

In the year1580 Alexander who was the proud Sixteenth Chief of the Innes clan was arrested and charged with murder of Walter Innes. He was found guilty at trial and executed by the Regent Morton. He was succeeded by his brother John, who resigned the Chieftainship and asked for it to be passed to his cousin Alexander Innes of Crommey. During a severe family quarrel, in the year of 1580 in Aberdeen , Alexander Innes was murdered by his kinsman Robert Innes of Innermarkie.

Sir Robert, twentieth chief was a privy councillor who represented Moray in Parliament was made a baronet of Nova Scotia by Charles the second in the year1625, which he later received at the Port of Garmouth which he founded in 1650. Although he was a prominent covenanter, he welcomed the uncrowned Charles the second at Garnoch in the year 1650, and raised a regiment to fight the royalist cause. Sir Robert Innes was responsible for the sale of Aberchirder estates but he was also the man who would build Innes House.

Over the years there have been many branches to the Innes clan, from Sir Robert Innes of that Ilk sprang the Baronets of Balveny in the year1628, and the Baronets of Coxton in the year of 1686. From Robert of Drainie came the Innes clan of Drumgask, and Balnacraig of who was Father Lewis Innes, the Jacobite secretary of State. These branches were all loyal to the house of Stuart in their struggle for right, as were the Inneses of Cathlaw.

Sir James, sixth Baronet and twenty-fifth Chief sold the lands of Innes to the Earl of Fife in the year 1767 and went to reside in England , only to return to Scotland when he succeeded as fifth Duke of Roxburgh in the year 1805. James, sixth Duke was created Earl Innes in the year 1836. Of the cadet branches the Barchets of Balvernie descend from Walter Innes of Innermarkie, son of Sir Robert Innes, eleventh of that Ilk; and the Innes of Coxton, a branch of Innermarkie are renowned for building the remarkable Tower of Coxton near Elgin in the sixteenth century.