Sir Theophilus Jones, (circa 1606–1610 to 1685) was an Irish soldier and government official of Welsh descent. One of five sons born to Lewis Jones, Bishop of Killaloe in the Church of Ireland, he formed part of a close-knit and powerful Protestant family. A grandson of James Ussher, head of the Church of Ireland from 1625 to 1656, in 1648 he married his cousin Alicia Ussher, another of his grandchildren. Of his four brothers, Henry and Ambrose were also bishops in the Church of Ireland, while Michael and Oliver were senior soldiers and politicians.