Haloperoxidases are used to selectively bind to and, in the presence of peroxide and halide, inhibit the growth of target microbes without eliminating desirable microbes or significantly damaging other components, such as host cells, in the environment of the target microbe. When a target microbe, e.g., a pathogenic microbe, has a binding capacity for haloperoxidase greater than that of a desired microbe, e.g., members of the normal flora, the target microbe selectively binds the haloperoxidase with little or no binding of the haloperoxidase by the desired microbe. In the presence of peroxide and halide, the target bound haloperoxidase catalyzes halide oxidation and facilitates the disproportionation of peroxide to singlet molecular oxygen at the surface of the target microbe. The lifetime of singlet molecular oxygen restricts damage to the surface resulting in selective killing of the target microbe with a minimum of collateral damage to the desired microbe or physiological medium. The methods and compositions of the invention are highly useful in the therapeutic or prophylactic antiseptic treatment of human or animal subjects, since their use can be designed to be highly effective in combatting bacterial or fungal infections without significant damage to normal flora or host cells. Suitable haloperoxidases include myeloperoxidase (MPO), eosinophil peroxidase (EPO), lactoperoxidase (LPO), chloroperoxidase (CPO) and derivatives thereof capable of selective binding to target microbes.