Knox was survived by his five children and his second wife. Nathaniel and Eleazar, his two sons by his first wife, attended St John's College, Cambridge. Nathaniel became a Fellow of St John's but died early in 1580. Eleazar was ordained into the Church of England and served in the parish of Clacton Magna. He also died young and was buried in the chapel of St John's College in 1591. Knox's second wife, Margaret Knox, got remarried to Andrew Ker, one of those involved in the murder of David Rizzio. Knox's three daughters also married: Martha to Alexander Fairlie; Margaret to Zachary Pont, son of Robert Pont and brother of Timothy Pont; and Elizabeth to John Welsh, a minister of the Kirk.;
