The unique properties of nanoparticles (NPs) and their interactions with biological systems, especially in biochemical reactions, provide many potential applications in molecular biology methods. Most of works have focusedon gold NPs only, and many other kinds of NPs such as silver (Ag) and titanium dioxide (TiO2) NPs have been largely neglected. Therefore, in this study, we evaluated the effect of Ag-NPs and TiO2-NPs on the real-time PCR (RTi-PCR) detection of four Aspergillus spp., A. flavus, A. parasiticus, A. ochraceus, and A. fumigatus, and four aflatoxin biosynthesis genes (tub1, aflR, aflD, and aflM) in A. flavus. Several combinations of Ag-NPs and TiO2-NPs at 3 mu L and 5 mu L were tested. The results showed that the Ag-NPs alone exhibited partial inhibition of RTiPCR at 3 mu L. Combinations of Ag-NPs and TiO2-NPs (1: 1, 2: 1, 3: 1) also partially inhibited RTi-PCR, but TiO2-NPs alone and their combinations with Ag-NPs (2: 1 and 3: 1) caused complete RTi-PCR inhibition. All combinations of Ag-NPs and TiO2-NPs at 5 mu L resulted in complete inhibition of RTi-PCR, except for the 2: 1 combination of Ag-NPs to TiO2-NPs. The results indicate that effects on the assay detection system must be carefully evaluated before Ag-NPs and TiO2-NPs are included in any RTi-PCR assay.