Known individuals who hold the name Jonathan include:
- Jonathan Shadowhunter, the most famous Shadowhunter with the name Jonathan as he is believed, according to legend, to be the first ever Shadowhunter;
- Sebastian Morgenstern, born Jonathan Christopher, the son of Jocelyn Fairchild and Valentine Morgenstern;
- Jonathan Wayland, the deceased son of Michael Wayland;
- Jace Herondale, the son of Céline and Stephen Herondale who was raised as Jonathan Wayland and believed to be Jonathan Morgenstern;
- Jon Cartwright, a former student at the Shadowhunter Academy and Centurion;
- Johnny Rook, a Herondale who hid in plain sight among mundanes and Downworlders;
- Kit Herondale, Johnny's son and namesake;
- Jonathan Clark, the name of the man Jocelyn claimed to be Clary's father for years.
- Another Jonathan, this time not from within The Shadowhunter Chronicles, is Jonathan Rhys Meyers, the actor who portrayed Valentine in The Mortal Instruments: City of Bones.