The Scots' Wars of Independence arguably began in 1286, when the English king Edward I used the death of King Alexander III as an opportunity to try and extend his influence in Scotland. Edward gained much ground throughout his reign, but following his death, the fortunes of the Scots began to improve, particularly in the wake of the Battle of Bannockburn (1314). At this time, though, the castles of Jedburgh, Roxburgh and Berwick remained in English control.

During the fifteenth century, a series of rebellions in England gave the Scots an opportunity to reclaim at least some of their lost territories. In 1408, the Scots managed to recapture Jedburgh Castle. Roxburgh Castle was won in 1460, during the Wars of the Roses, but the cost was high: King James II died at the siege when a cannon exploded, mortally wounding him. 1461 saw the return of Berwick to Scots' control, but it was later recaptured by the English in 1482.

King James IV was determined to recapture Berwick, and during his reign he led several incursions into English territory. Though he was married to Margaret Tudor, sister of King Henry VIII, James allied himself firmly with the French. James died in1513 at the Battle of Flodden, an event which can arguably be seen as the worst military disaster in Scottish history.

James' son, King James V, continued the 'Auld Alliance' with France by marrying Mary of Guise. His early death in 1542 resulted in another precarious period for Scotland, with the kingdom left to an infant girl, Mary, Queen of Scots. King Henry VIII saw this as a welcome opportunity to bring Scotland into his control by ensuring a marriage between Mary and his own young son, Edward. When diplomacy failed to bring an agreement with the Scots, he resorted to force. The end result became known as 'the Rough Wooing': during this period, much of the Merse was burned and looted by soldiers commanded by the Earl of Hertford. Documents still survive which record the extent of this destruction.

Following Henry's death, the reign of Queen Elizabeth I brought a period of comparative peace between Scotland and England. In the Border lands, however, lawlessness continued at the hands of the reivers, who robbed and plundered widely, and engaged in violent and bloody feuds. When King James VI became James I following the Union of the Crowns in1603, there was a concerted effort to curtail the activities of the reivers, but violence re-erupted in the religious wars of the mid-sixteenth century. Those with Covenanting sympathies inevitably supported the side of Parliament during the Civil War, with some prominent Border families, such as the Baillies of Jerviston and the Humes of Marchmont, paying a heavy price for their involvement. It was only when King William III succeeded to the throne at the expense of James VII in 1688 that there was an end to almost four centuries of violence and unrest in the Borders.