He was the son of Morys Wynn ap John, who he succeeded in 1580, inheriting Gwydir Castle in Carnarvonshire. John was educated at All Souls College, Oxford (1570, awarded BA 1578) and studied law at Furnival's Inn (1572) and the Inner Temple (1576). He claimed to be directly descended from the princes of Gwynedd through Rhodri ab Owain son of Owain Gwynedd. The male line from his family died out in 1779 (see 'Legacy' section below) and the senior male line passed to the Anwyl of Tywyn family. His mother was Jane (Siân) Bulkeley, daughter of Sir Richard Bulkeley and his wife Catherine Griffith, and sister of Sir Richard Bulkeley, head of the Anglesey branch of a powerful landowning family, who originally came from Cheshire.