Jonathan could refer to:
- People
- Jonathan, a resident of "The Frontier" colony
- Jonathan Archer, fifth President of the United Federation of Planets
- Jonathan Archer (mirror), leader of Archer's Rebellion against the Terran Empire
- Jonathan Chen, a lieutenant aboard the USS Enterprise
- Jonathan DeNoux, a lieutenant aboard the USS Odyssey
- Jonathan Esteban, CO of the USS Grissom
- Jonathan Galt, a Starfleet Intelligence chief of staff stationed on Vulcan
- Jonathan Hart, father of Enterprise NX-01 security officer Alana Hart
- Jonathan Lense, fraternal twin brother of Elizabeth Lense
- Jonathan Pollard, chairman of the biology department at Starfleet Academy
- Jonathan Raymond, a relative of Clare Raymond
- Jonathan Sisko, son of Benjamin Sisko and Kasidy Yates
- Jonathan Soto, CO of the USS Sovereign
- Jonathon Stanger, security chief of the USS Victorious
- Jonathon Stone-Whistle, a former Starfleet officer
- Jonathan Struhlem, an officer aboard the USS Enterprise-E
- Jonathan Swift, author of Gulliver's Travels
- Jonathan Vance, a 24th century temporal scientist
- Jonathan Walker, a computer technician on Sheridan's World
- Johnathon Walsh (23rd century), a Starfleet weapons officer
- Johnathon Walsh (24th century), a 24th century Starfleet weapons officer
- Jonathan Willis, CO of the USS Khitomer
- Starships
- USS Jonathan T. Esteban, a Decker-class destroyer
- Real-world topics
- Jonathan Bridge, a Strange New worlds contest winner
- Jonathan Frakes, a director, the actor who portrays William T. Riker
- See also: John
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