Fungal contamination of drinking water has become a major water quality concern in recent years and as a result, various disinfection methods have been explored. A promising, but relatively unexplored disinfection approach, is the combination of potassium peroxymonosulfate (PMS) with chloride (Cl-) to inactivate fungal spores. In this study, four dominant fungal species found in groundwater were selected to evaluate the efficacy of PMS/Cl- disinfection combination system. The PMS/Cl- system exhibited a delayed Chick-Watson model to inactivate the four genera of fungi and had an improved sustained inactivation effect than a Cl-2 system despite the lag period. Four genera of fungi resist PMS/Cl- inactivation to varying degrees: Trichoderma harzianum > Aspergillus niger > Penicillium polonicum > Cladosporium cladosporioides, which was found to be related to their hydrophobicity and individual size. Inactivation of fungi by the PMS/Cl- system was enhanced with increasing PMS or Cl- dosage and also lower pH, but was inhibited by the presence of humic acid (HA). The main reactive species are HOCl/OCl- but not the reactive radicals responsible for the inactivation of fungal spores. The increase of extracellular proteins, total dissolved nitrogen, extracellular adenosine triphosphate and morphologic changes of the four genera of fungi prior to and after inactivation, revealed that the cell membrane of fungal spores was damaged seriously by exposure to the PMS/Cl- system. Moreover, PMS/Cl- system also exhibited a good inactivation effect on the four genera of fungi in real groundwater. Finally, attention should be paid to the use of phosphate buffer solution containing Cl(- )when PMS is used for disinfection experiments as this could impact results.