The clan name is a territorial name derived from the lands of Blackadder in Berwickshire. The lands, in turn, are named after the Blackadder Water, a river which is part of the River Tweed system, and which runs through the Scottish Borders. The name Blackadder is derived from the Old Englishawedur which means "running water" or "stream". George Fraser Black states that in 1426, Blakadir de Eodem held the lands in the earldom of March. Early bearers of the surname are Adam of Blacathathir in 1477, Robert Blackader in the 15th century, and Charles Blakater in 1486.
The Blackadders of that Ilk were Border Reivers, involved in the deadly raids and feuds along the Anglo–Scottish border during the 15th and 16th centuries. Their base by the Blackadder Water was near Berwick-upon-Tweed, a town that changed hands 13 times between England and Scotland in the period 1147–1482. The family gained lands from James II of Scotland in reward for their deeds in repelling in English raids. In 1518 the family lost their Border lands by the forced marriages of the two heiresses of Robert Blackadder of that Ilk to the neighbouring Clan Home. This process became known as "the fraud of the Homes". According to the 19th-century historian William Anderson, the marriages were achieved in the following way. . This process was challenged by a Blackadder kinsman, Sir John Blackadder who held the lands of Tulliallan. He attempted to gain assistance from the Parliament, and also attempted to use force to regain the former Blackadder possessions. In March 1531, he was beheaded for the murder of the Abbot of Culross, in the dispute. Sir John Blackadder was succeeded by his brother Patrick, who also took action to regain the lands from the Homes. Anderson's version of events has Patrick ambushed and murdered by the Homes, while he was attempting to meet them and resolve the dispute. By 1567 the dispute had died down, as the Tulliallan branch and the Homes of Wedderburn were allies of Mary, Queen of Scots on the losing side in the important Battle of Carberry Hill. After the battle Mary abdicated as queen. Subsequently, the Blackadders relinquished their claim to the Border lands, and in 1671 Sir John Home was created Baronet of Blackadder. Some members of the clan continued to farm their lands as tenants of the Homes, and the last family burials at Edromkirk were made in the 1980s. William Francis Blackadder played in the Scottish rugby team in 1938, and was awarded the DSO and OBE as an RAF ace in World War II.