The company was established as Mid-Hudson Airlines-.
In 1984 it began transitioning into operating in affiliation with American Airlines, much like AmericanConnection does today. By maintaining independent management and separate ownership, it continued to do business in its own colors as Command Airways, although its fleet was primarily dedicated for American Airlines operations. This permitted Command to gain marketing presence associated only usually with much larger airline carriers.
Command was the first airline to carry the American Eagle brand when it became a part of the American Eagle system which included repainting their entire fleet under the American Eagle banner. This rebranding process of regional airlines commenced circa 1985 and accelerated when American Airlines parent company began purchasing a number of smaller regional carriers after the bankruptcy (December 1987) of one of its affiliate partners named Avair, which was operating similarly to Command Airways.
AMR Corporation the parent company of American Airlines, purchased Command Airways in 1988 and renamed it Flagship Airlines. This and other AMR affiliate and subsidiary airlines and Flagship Airlines flew under the American Eagle banner before all parties began being referred to more simply as American Eagle in 1991.
Command/Flagship Airways was operated separately until all AMR subsidiary regional carriers excluding Executive Airlines were merged into a commonly certificated carrier name American Eagle Inc. in late 1998, utilizing the former Simmons Airlines two letter IATA Code.
During its existence, Command Airways operated the Beech 99, DeHavilland Canada Twin Otter, Shorts 330, Shorts 360-300 and ATR-42 airliners. Command was the first U.S. airline to operate both the Shorts 330  starting in 1976 and the ATR-42 beginning in 1986.
Its hub was at the Dutchess County Airport in Poughkeepsie, which no longer has scheduled commercial airline service today.
- New York
- New Hampshire
Those articles marked with an asterisk (*) are no longer served by commercial airline service.
- Information about Command Airways at the Aviation Safety Network
- "COMPANY NEWS; AMR Acquisition". The New York Times. 14 June 1988.