In the autumn of 1562, Mary, Queen of Scots came to the north to punish the family on the basis of allegations against Jean's brother, Sir John Gordon.

At Darnaway Castle, Mary gave Huntly's title of Earl of Moray to her own illegitimate half-brother James, who was the husband of Jean's first cousin, Lady Agnes Keith.

Jean's father slipped away from Huntly Castle, evading the queen's soldier William Kirkcaldy of Grange, but was defeated by James at the Battle of Corrichie in 1562.

Jean's father was posthumously tried for treason in Edinburgh, where his embalmed body was brought to face parliament, and his title and lands were thereby forfeited to the crown.

[4] Jean's eldest surviving brother, Lord Gordon, was spared execution and eventually allowed to succeed the rebel Earl.

On 24 February 1566, Jean, who was a Catholic, married James Hepburn, 4th Earl of Bothwell, in a Protestant-rites ceremony apparently celebrated with considerable pomp.

Queen Mary, who strongly approved of the match, supplied cloth of silver and white taffeta for Jean's wedding gown, although she had wanted the marriage to have taken place in the Chapel Royal during a mass.

[8] According to author Antonia Fraser, she had a "cool, detached character warmed by a masculine intelligence, and a great understanding above the capacity of her sex.

[17] Following Bothwell and Queen Mary's defeat at Carberry Hill, Jean abandoned Crichton, and returned to her mother at Strathbogie Castle.

In 1630 the garden at Dunrobin was described as "planted with all kynd of fruits, hearbs and flowres used in this kingdome, and good store of sfaron, tobacco and rosemarie".

Irish actress Maria Aitken played the part of Jean Gordon, Countess of Bothwell in Mary, Queen of Scots, the 1971 film which starred Vanessa Redgrave in the title role.