By David L. Phillips

Nearly 93 percent of Iraqi Kurds voted for independence in the referendum on September 25. Now Washington faces a choice. The U.S. can either support the Iraqi Kurds who are staunch allies. Or it can back Iraq, a sectarian theocratic state acting as a proxy for Iran.

Premier Heider al-Abadi became prime minister in 2014, with endorsement from Iran’s National Security Council and support from President Hassan Rouhani. Abadi’s predecessor, Nouri al-Maliki, was a deeply polarizing figure, also backed by Tehran. Iraqi parliament speaker Salim al-Juburi works closely with his Iranian counterpart, Ali Larijani, a staunchly conservative politician and former military man.

Close security cooperation bind Iran and Iraq. The Iraqi armed forces and the Iranian Revolutionary Guard Corps (IRGC) are shoulder-to-shoulder in the fight against ISIS. Just a few days ago, Iran and Iraq held a joint military drill on Iraqi Kurdistan’s border, warning their “common enemy”.

Shiite militias, the Popular Mobilization Forces Militias (Hash’d al Shaabi) were created via a fatwa by Grand Ayatollah Ali al-Sistani, extolling their “sacred duty” to liberate Mosul from ISIS. Shiite militias in Iraq are responsible for the deaths of many Americans.

Other Iraqi paramilitary units also threaten U.S. forces. The Peace Brigades are loyal to the virulently anti-American Iraqi cleric Moqtada al-Sadr. The Badr Organization is a well-armed Iranian proxy militia.

ISIS was an economic bonanza for Iran. Iran’s Trade Promotion Organization reports that Tehran’s non-oil exports to Baghdad grew from $2.3 billion in 2008 to $6.2 billion in 2015 during which time Iraq helped Iran access global markets in violation of international sanctions.

Iran and Iraq also cooperate extensively in the energy sector. On September 25, the day of Iraqi Kurdistan’s referendum, Iraq’s Oil Minister Jabbar al-Luaibi announced a major investment in two new joint oil production facilities.

While the Trump administration condemns Iran’s support for terrorism, it effectively supports Iran by aligning itself with Iraq. Secretary of State Rex Tillerson mistakenly calls Iraq “united, federal, and democratic.” Backing Baghdad, he criticized Iraqi Kurdistan’s independence referendum for lacking “legitimacy.”

Iraq is not “united”. Iraqi Kurdistan has enjoyed de-facto independence since 1991. Deep sectarian divisions exist between pro-Iranian Shiites and Iraqi Sunnis, many of whom support ISIS.

Iraq is not “federal”. A recent study found 55 violations by Baghdad of its federal constitution. The Iraqi government repeatedly refuses to implement Article 140, which requires a referendum on the status of Kirkuk.

Iraq is far from “democratic”. Its Shiite majority exerts majoritarian rule, disenfranchising both Sunnis and Kurds.

The U.S. Congress is increasingly aware of Iran’s nefarious influence. Senator Chuck Schumer, the Democratic minority leader, accused “[Iraq]’s neighboring countries, led by despots who oppose a Kurdish State because it threatens the status quo and their self-interests.” Senator John McCain supports a political process that addresses the aspirations of the Kurds for an independent state. They understand that Iraqi Kurdistan is a bulwark against Iranian influence.

A “sense of the Congress” resolution should call on the United States to recognize Iraqi Kurdistan if/when it declares independence.

The Congress should provide a direct appropriation to Kurdistan’s peshmerga. Increasing the supply of heavy weapons would deter an attack by the Iraqi armed forces and Shiite militias.

The Congress should also restrict the transfer of heavy and offensive weapons to Iraq, which fall into the hands of Iranian-backed militias.

U.S. policy is at a fork in the road. Washington should align itself with Iraqi Kurdistan, supporting democracy and the national aspirations of Iraqi Kurds

Mr. Phillips is director of the Program on Peace-building and Rights at Columbia University’s Institute for the Study of Human Rights. He served as a Senior Adviser and Foreign Affairs Experts to the Near Eastern Affairs Bureau of the State Department, working on the Future of Iraq Project. He authored Losing Iraq: Inside the Post-War Reconstruction Fiasco.