In theory and usual practice, the Governor of the State. He or She ( some states have had female governors- like New Jersey under Whitman) can call out the National Guard to control civil emergencies such as riots, etc. However, as the President of the United States has CINCUS ( Commander In Chief- US) he can and does have the authority to federalize NG units which are technically a part of the US Army and dispatch them on various missions- one peacetime example was the Federalization of guardsmen to contain racial problems in Little Rock, Arkansas during the Desegregation battles. This is the best known action of the type- unlike deployment of Guard units to foreign wars- for example stop-loss assignments in Iraq.
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The Governor of Alabama, which is currently Robert R. Riley.
The President is the Commander-In-Chief of the Armed Forces, not of the United States.
The commander in chief of the united states is Barrack Obama.
At state level, it would be the State Governor, who serves as Commander in Chief for their state's respective military department, or whichever department the National Guard and State Guard/State Defence Force (if their state has one) is relegated under.
The President is the Commander-in-Chief and utlimate head of the armed forces of the United States.