Dee was born in Tower Ward, London, to Rowland Dee, of Welsh descent, and Johanna, daughter of William Wild. His surname "Dee" reflects the Welsh "du" (). His grandfather was Bedo Ddu of Nant-y-groes, Pilleth, Radnorshire; John retained his connection with the locality. His father Roland was a mercer and gentleman courtier to Henry VIII. John Dee claimed descent from Rhodri the Great, Prince of Wales, and constructed a pedigree accordingly. His family had arrived in London with Henry Tudor's coronation as Henry VII.