Earlier this month when President Obama visited a mosque, he gave a message of “religious tolerance and unity.” He talked about how “Islam has always been part of America.” He even pointed out that: “Thomas Jefferson wrote in the Virginia statute for religious freedom that the Mohammedan should have his faith protected in the United States.”

While that is true, there is another part of the Thomas Jefferson story that most Americans do not know. Our third president actually declared war on the Muslim pirates who were from the Barbary Coast of Tripoli, Tunis, Morocco, and Algiers.

Before the Revolutionary War, American ships had been under the protection of England. Then the United States had to provide protection, but the Barbary pirates began to capture many of the ships. The United States (along with many European governments) began paying bribes to the Barbary States.

When Thomas Jefferson became president, the Pasha of Tripoli sent a note demanding the immediate payment of $225,000 a year plus additional amounts in future years. That was enough. Jefferson told the Pasha what he could do with the demand. The Pasha cut down the flagpole in Algiers and declared war on America. The other Barbarian States also declared war.

Congress and the president then responded by empowering American ships to seize all vessels and goods of the Pasha of Tripoli. Once the U.S. took action some of the other Barbary States backed down. But the war with Tripoli last four more years. This included a battle in 1805 when the Marines raised the American flag not far from the shores of Tripoli. That, of course, is the famous line in the anthem of the Marine Corps.

The president told one story about Thomas Jefferson and Islam. You have now heard the other story often ignored.