Objective To investigate the effects of cinnamaldehyde and citral on DNA and RNA of Aspergillus flavus and A. fumigatus cells and their mechanisms. Methods A. flavus and A. fumigatus were incubated on Czapeks agar plate (treated with cinnamaldehyde and citral at different concentrations) at 26.5 ℃ for 3—6 d. The normal and treated cells were observed by laser scanning confocal microscope (LSCM) and image analysis to describe the DNA and RNA levels by quantity and localization. Results DNA and RNA levels were changed greatly and multinucleate coniospores appeared in the treated cells. Conclusion Cinnamaldehyde and citral have directly or indirectly interfered the conventional synthesis of fungal hereditary DNA and RNA and normal differentiation of conidiophore in A. flavus and A. fumigatus, thus inhibiting the normal cell cycle and the growth and propagation of fungi.