The filamentous fungus Neurospora crassa is a global model for genetic research. The analyses of its 5S RNA genes' composition and distribution across the genome revealed the genomic defense system RIP (repeat-induced point mutation). And by analyzing its mutated 5S RNA pseudogenes, one important epigenetic modification, DNA methylation, was identified. Subsequent research made Neurospora crassa as one of the most extensive model organisms for investigation the mechanism of DNA methylation among the eukaryotes. During its vegetative growth stage, the homologous genes silencing (quelling) caused by transgene was demonstrated to be regulated by RNA interference which was exhibited to play a key role in meiotic silencing. The features of Neurospora crassa including its streamlined genome and the same DNA methylation and histone modifications as the higher eukaryotes will make it an important model organism to further research the epigenetic regulation of gene expression and genome stability.