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The name originates in the Houston barony in Lanarkshire.

The family were originally called Paduinan, from a place name also in Lanarkshire. Hugh de Paduinan received the lands of Kilpeter from Baldwin de Bigre during the reign of Malcolm IV. By the time of Hugh's grandson (also Hugh) the land became known as the barony of Houston, or Hugh's Town. Fynlawe de Hustone, knight, of Lanarkshire rendered homage in 1296 to Edward I of England, along with a number of other of Scotland's nobility, with the signing of the Ragman Rolls.

During the 16th century's Anglo-Scottish Wars, Sir Peter Huston fought along side Matthew Stewart, the 2nd Earl of Lennox, at the Battle of Flodden in 1513, where, subsequently, both men died. Sir Peter's son, Sir Patrick was the Keeper of the Quarter Seal, and companion to James V, but working with Lord Lennox, the two plotted against their king. He was eventually killed at the Battle of Linlithgow Bridge in 1526, which also saw Lennox captured and murdered by James Hamilton of Finnart.

According to 'Surnames of Scotland' by George Black, people of this name in the Canisbay district are descended from Rev. Andrew Ogstoun of Canisbay, Caithness, while the Houstons of Ross-shire are believed to be descended from Rev. Thomas Houston of Inverness (died 1605).

The sons of the fifth Huston Baronet had done a lot to increase greatly the family's colonial estates, and at the time when independence was granted to the American colonies from Great Britain, it was said that they owned over eight thousand slaves. This line of Hustons went on to disown their Scottish titles with preference for their American wealth.

A prominent figure in the fight for Texan independence from Mexico, General Sam Houston, was a descendent of these Hustons. He went on to become the first President of the Republic of Texas, and later on the Senator for Texas when they agreed to join the United States in 1845.