John Sinclair, Master of Caithness was the eldest son of George Sinclair, 4th Earl of Caithness and his wife Lady Elizabeth Graham, daughter of William Graham, 2nd Earl of Montrose. His father, George, Earl of Caithness had feuded with the Earl of Sutherland and the Murrays of Aberscross which had resulted in the Battle of Torran-Roy in 1570 where Caithness was defeated, but returned to besiege the Murrays at Dornoch where several of them were subsequently beheaded. John Sinclair, Master of Caithness was later imprisoned by his father for making peace with the Murrays. The Master of Caithness died at Castle Sinclair Girnigoe in 1576.
In 1543, John Sinclair, Master of Caithness had obtained a charter from Mary, Queen of Scots by which the Earldom of Caithness became a male fee, to him and his male heirs. He married Jean Hepburn, daughter of Patrick Hepburn, 3rd Earl of Bothwell and had the following children:
- George Sinclair, 5th Earl of Caithness.
- James Sinclair, 1st of Murkle.
- John Sinclair, 1st of Greenland and Rattar.
- Agnes Sinclair.
- Henry Sinclair, a natural (illegitimate) son, who married Janet Sutherland and had a son, John, who is probably the ancestor of the Sinclairs of Lybster. Henry Sinclair accompanied George, Earl of Caithness in an expedition to Orkney, where, whilst besieging Kirkwall Castle, he died in bad health.
- According to Henderson, a historian named Douglas gives the Master of Caithness another legitimate son named David, but that this is an error. However, Henderson does confirm that this David Sinclair was the laird of Stirkoke who descended from an illegitimate son of George Sinclair, 5th Earl of Caithness and who was the father of George Sinclair who was killed in an expedition to Norway in 1612.
- Henderson, John W.S (1884). Caithness Family History. Edinburgh: David Douglas. pp. 5-7.
- Maclauchlan, Thomas, 1816-1886; Wilson, John, 1785-1854; Keltie, John Scott, Sir, 1840-1927 (1875). A History of the Highlands and of the Highland Clans. 1. Edinburgh: T.C. Jack. pp. 92-93.
- Way, George of Plean; Squire, Romilly of Rubislaw (1994). Collins Scottish Clan & Family Encyclopedia. HarperCollins Publishers. pp. 322–323. ISBN 0004705475.
- Henderson, W.S (1884). pp. 5-6 and 103.