The main difference between skirt steak and flank steak is where the steak is cut from the cow.
Skirt steak is a thin, long cut of beef from the diaphragm muscles of the cow while Flank Steak is cut from the abdominal muscles or lower chest of the cow.
Skirt steak also has a more beefy flavor than Flank steak does and has more tough muscles than Flank steak too.