The 50-year-old was arrested Saturday by Jacksonville police and charged with larceny after he allegedly took printer cartridges and a bottle of auto engine treatment from a Wal-Mart store.
He's scheduled to appear in court in February.
A Marine Corps spokesman says they are cooperating with civilian authorities and that they take such allegations very seriously.
It's the second high profile arrest of a Marine Corps commander in recent months.
Last week, the Marine Corp announced it was considering military charges for the former commander of Marine Corps Air Station Cherry Point.
Colonel Douglas Denn had already been relieved of his command after a drunk driving arrest last year.