The new chief, Gen Mohammad Ali Jafari, commanded the Revolutionary Guards ground forces for 13 years.
His predecessor, Gen Yahya Rahim Safavi, has been appointed a special military adviser to Ayatollah Khamenei.
The decision comes just two weeks after
The Revolutionary Guards condemned the plan as "worthless resolutions" issued "under baseless pretexts... to damage this holy institution".
'Natural' change
In a decree issued on Saturday, Ayatollah Khamenei pointed to Gen Jafari's "brilliant background in the armed forces in different stages", state-run media reported.
The 50-year-old reportedly won both popularity and respect among the guards for his role as a commander during the 1980-1988 war with
No reason was given for the surprise move, but Iranian officials insisted the change was routine and that Gen Safavi's appointment should be seen as a promotion.
"Appointments made by His Eminence are usually for no longer than 10 years," Gen Safavi told the Iranian television channel, IRTV1. "Such movements are natural."
The Revolutionary Guards force was set up shortly after the 1979 Iranian revolution to defend the country's Islamic system, and to provide a counterweight to the regular armed forces.
It has since become the dominant military force in
It is estimated to have 125,000 active members, and boasts its own ground forces, navy and air force. It also controls the paramilitary Basij Resistance Force and the powerful bonyads, or charitable foundations, which run a considerable part of the Iranian economy.
The
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Gen Mohammad Ali Jafari