Small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs) play crucial roles in post-transcriptional gene silencing (PTGS) in eukaryotes. Small RNAs function cell-autonomously as well as non-cell-autonomously. It has been well characterized that pathogenic fungi secrete some effector molecules, which facilitate their infection into plants. However, it is not clear whether molecules in plant cells are able to move into fungal cells during infection. To test if small RNAs generated from plant cells can also move to fungal cells during infection, we generated transgenic Arabidopsis and rice plants ectopically expressing either double-stranded RNA interference (dsRNAi) or artificial miRNA (amiRNA) constructs targeting GFP gene. And then these transgenic plants were inoculated with transgenic rice blast fungus, Magnaporthe oryzae, expressing GFP transgene. Here, we showed that ectopic expression of both dsRNAi and amiRNA targeting GFP gene in transgenic plants significantly suppressed GFP expression in rice blast fungi inoculated, indicating that small RNA molecules generated in plant cells can move into infected fungal cells and efficiently degrade fungal GFP transcripts. Our results would provide a new small RNA-based strategy for the development of resistant crops against fungal pathogens.