The lines can be blurred, as when the Lunar Reconnaissance Orbiter began as a directed mission from the HEOMD, and was later transferred to the SMD.
Unlike these competed classes that tender proposals through a competitive selection process, the development of Flagship missions is directed to a specific institution — usually a NASA center or the Jet Propulsion Laboratory — by the Science Mission Directorate.
[2][1] Flagship missions are developed ad-hoc, with no predetermined launch cadence or uniform budget size.
[2] Of the four Great Observatories, only the Spitzer Space Telescope is not a Flagship mission.
Initially budgeted at US$2 billion, Spitzer was downscoped to a medium-size mission of US$720 million.