The al-Houthi rebels, a group of Shiite dissidents, have refused to recognize the Yemen central government's authority and call for a return to a Shiite Islamic governing system similar to Iran's, Bikyamasr.com said.
Amid unrest in Yemen, the al-Houthi rebels have in recent months extended their hold in three northern Yemen provinces, Sa'ada, al-Jawf and Hajjah.
Officials told Bikyamasr.com "heavy weapons were on board" the Iranian ship.
Al-Watan, a Kuwait newspaper, reported the ship carried mortar launchers, anti-armor shells and other weapons.
The al-Houthi rebels have faced heavy resistance from Salafists, a group of Sunni Islamic hardliners supported by Saudi Arabia, but the rebels have made significant inroads.
The al-Houthi have kidnapped Saudi rebels and conducted raids against villages on the northern Yemen-Saudi border, the site of past tensions.
The capture of the Iranian ship comes as Iran conducts more military exercises in the strategic Strait of Hormuz, which Tehran has threatened to block.
U.S. officials have said Iran could be attempting to rely on al-Houthi rebels to advance its cause in the region. If Iran won Yemen as an ally, it would have direct access to the Red Sea, which is near the Suez Canal and an international oil route as well as Israel.