We report a ratiometric fluorescent sensor based on monochlorinated BODIPY for highly selective detection of glutathione (GSH) over cysteine (Cys)/homocysteine (Hcy). The chlorine of the monochlorinated BODIPY can be rapidly replaced by thiolates of biothiols through thiol halogen nucleophilic substitution. The amino groups of Cys/Hcy but not GSH further replace the thiolate to form amino-substituted BODIPY. The significantly different photophysical properties of sulfur- and amino-substituted BODIPY enable the discrimination of GSH over Cys and Hcy. The sensor was applied for detection of GSH in living cells.