The Treasury placed sanctions on Shahid Nuri Industries and Shahid Movahed Industries, both units of the Shahid Hemmat Industrial Group the US says is responsible for Iran's liquid-fueled ballistic missile program.
It also sanctioned the Al-Ghadir Missile Command of the Islamic Revolutionary Guard Corps (IRGC), which it said appears to have operational control of the country's ballistic missiles.
The US actions were based on broader sanctions over the country's alleged ties to terror activities. Sanctions tied to its nuclear activities were lifted in January as part of a deal with major powers.
"Iran's ballistic missile program and its support for terrorism pose a continuing threat to the region, to the United States, and to our partners worldwide," said Adam Szubin, Treasury's acting undersecretary for terrorism and financial intelligence.
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"We will continue to use all of our tools to counteract Iran's ballistic missile program and support for terrorism, including through sanctions."
The sanctions freeze any assets of the listed entity under US jurisdiction and ban any business with them by US companies or individuals.
Mahan Air "continues to support the Iranian government's destabilizing actions in the region by conducting flights to Syria in order to transport fighters," the Treasury said.
In Tehran, the foreign ministry blasted the new US moves.
"The Iranian ballistic missile program has nothing to do with the nuclear agreement and does not violate" the UN Security Council resolution, said spokesman Hossein Jaber Ansari.