This course will begin with the basics of the study of the Anti-Self-Dual Yang-Mills equation.  We'll emphasize the parts of the theory important for setting Floer homology for three manifolds and also for links in three manifolds.  We'll show how to extend the theory to sutured manifolds and cover the surgery exact sequences for these theories.  We'll see that these theories can be used to detect knot genus and the Thurston norm. Using this background we'll relate Khovanov homology to a version of instanton Floer homology and deduce that Khovanov homology detects the unknot from the  corresponding result in the instanton theory.