Israel Stoughton (1603?-1644) was an early English colonist in Massachusetts and a colonial commander in the Pequot War. Returning to England, he served as Parliamentarian officer in the First English Civil War.
Born in England, a younger brother of John Stoughton, Stoughton emigrated to the Massachusetts colony in 1632. He settled at Dorchester and was admitted as a freeman there on 5 November 1633. Stoughton was chosen as representative for Dorchester in the Massachusetts General Court in 1634 and 1635.
During the height of the Antinomian Controversy in the colony, Stoughton wrote a book that attacked the colony's constitution. The book offended some members of the General Court, which barred Stoughton from holding any colony offices for three years. Stoughton later petitioned that the book be ‘forthwith burnt, as being weak and offensive.’ Despite this reversal, the General Court maintained their ban until 1836. In 1637, the General Court allowed Stoughton to become an assistant.
In 1636, war broke out between the Pequot tribe and the three New England colonies and their Native American allies. Appointed commander of the Massachusetts colony militia, Stoughton reportedly employed brutal tactics against the Pequot.
In 1639 Stoughton and John Endecott acted as a commissioners on behalf of Massachusetts Colongy to settle a boundary dispute with Plymouth Colony.
Toward the end of 1643, Stoughton made a quick trip to England, returning home by the beginning of 1644. However, by the end of 1644, he went to England again, never to return to Massachusetts
With the advent of the First English Civil war, the English Parliament appointed Stoughton as a lieutenant-colonel in their army. Stoughton died very soon afterwards in Lincoln.
Stoughton's children included William Stoughton, best known as the chief magistrate of the Salem witch trials in Massachusetts.