An aqueous nanoparticle suspension of a bis-methanophosphonate fullerene (n-BMPF) was tested to clarify its effects on polymerase chain reaction (PCR) with the catalyst of Taq DNA polymerase and DNA exonuclease Exo Ⅲ and the template of super-coiled plasmid pEGFP-N1. It was found that the product amounts from PCR decreased significantly with addition of the n-BMPF. The inhibition by the n-BMPF was dose-dependent and IC50 values for reactions of PCR were 2.7 μmol/L. Increase of Taq DNA polymerase amounts in PCR system antagonized the activities of the n-BMPF. However, addition of two scavengers of reactive oxygen species (ROS), mannitol and azide at the concentrations of 2~10 mmol/L did not antagonize the activities of the n-BMPF against PCR. These data implied that this inhibition probably did not correlate to ROS. Meanwhile, the inhibition for the DNA exonuclease Exo Ⅲ by the n-BMPF was evident and dose-dependent.