Horseradish peroxidase (HRP) is enzyme first described more than 200 years ago and yet there are still some aspects of this potent enzyme to be tackled. Researchers were focused on most abundant isoenzyme HRP C1A while remaining, particularly anionic isoenzymes were discarded in purification process. This work describes exploitation of those isoenzymes for removal of recalcitrant pollutants such as reactive dyes. Results demonstrated that not only these enzymes can decolorize dyes but also in some cases anionic forms are more efficient than commercially produced cationic HRP form. Enzyme concentration of 0.14 U ml−1 was found to provide maximum dye removal at optimized reaction conditions with dye concentration of 30 mg l−1. Majority of dyes tested were successfully decolorized at pH 5 or 7 while some dyes like Orange 2 and Reactive black 5 are decolorized most efficiently at pH 9. Anionic isoenzymes act by disrupting chromophore of Reactive black 5 while cationic HRP oxidize dye but leaves chromophore present.