Jones was born about 1570 to Christopher and Sybil Jones of Harwich, co. Essex, England. The Harwich records for the year of his birth are missing. Christopher was his father's eldest son. He lived in a house on High Street. Jones was eight years old when his father died. Christopher was left his father's share in the ship "Marie Fortune" when he turned eighteen. His brother Roger was left an eighth part and stock in another ship, the "Centurion", when he turned eighteen. Christopher's mother married Robert Russell on 20 September 1579.