Executive Order 9066 was an authorization for the secretary of war to create militarized zones that were to serve as concentration camps for the Japanese. It was issued in 1942 a few months after the attack on Pearl Harbor and created concentration camps that lasted until 1945.
During World War II (1939-1945) nearly 90% of the Japanese individuals living in the continental US were interned in these camps. Many of them were American citizens in the second and third generations.
Roosevelt passed this executive order because of the Japanese attack on Pearl Harbor. The order served to make any Japanese individual a potential spy working against the US.