"The secretary discussed heightened tensions in the region and the need for stronger maritime security in order to promote freedom of navigation," State Department spokeswoman Morgan Ortagus said in a statement.
Iran has seized three tanker ships in strategic Gulf waters in a month, and the United States has accused it of carrying out multiple attacks on ships in the region.
The US has been struggling to piece together an international coalition to protect cargo ships travelling through the Gulf, with allies concerned about being dragged into conflict with Iran.
Ortagus also said that the top US diplomat and the crown prince "discussed other bilateral and regional developments, including countering the Iranian regime's destabilizing activities."
Tensions between Washington and Tehran -- Saudi Arabia's arch foe -- have soared since US President Donald Trump pulled the United States out of a nuclear deal with Iran last year and imposed punishing sanctions.
Twelve months on from the US withdrawal, Iran responded by suspending some of its commitments under the nuclear deal.
Iran meanwhile shot down an American drone in June, with Trump saying he called off retaliatory air strikes at the last minute, and the United States says it has since downed one and possibly two of Tehran's unmanned aircraft, which the Islamic republic has denied.
On Yemen, "the secretary and the crown prince reaffirmed their strong support for UN Special Envoy Martin Griffiths' efforts to advance the political process," Ortagus said.
Saudi Arabia is locked in a bloody war in the country against the Iran-backed Huthis, a conflict that has killed tens of thousands of people, many of them civilians, relief agencies say.
Trump vetoed congressional resolutions last month that would have blocked arms sales to the kingdom that critics fear would aggravate the devastating Yemen war, which the UN said has triggered the world's worst humanitarian crisis.