In plants, virus infection and small RNA (sRNA) metabolism are closely associated. sRNAs are considered ‘master regulators of gene expression and constitute one of the most important defense mechanisms against foreign nucleic acids, such as viruses and viroids. In response to host defenses, most plant viruses have evolved mechanisms to interfere with sRNA biogenesis and activity, with broad effects on host homeostasis. This thesis includes studies on virus and viroid detection by searching for pathogen-specific nucleic acids and pathogen-derived sRNA products of the host defense machinery. Two short reports describe the detection of Spinach latent virus and Australian grapevine viroid. A third study describes the limited genetic diversity of Grapevine virus E infecting grapevines across the US. In a subsequent study, a combination of electron microscopy and next generation sequencing (NGS) technologies were used to elucidate the identity and complete genome sequence of another grapevine infecting virus, namely Grapevine asteroid mosaic associated virus; obtaining a full genome sequence allowed an examination and comparison of the genome’s functional domains and sequence signatures that reflect strategies for the expression and processing of the virus encoded proteins. Finally, to better understand the role of sRNAs in the regulation of gene expression, a genome wide evaluation was performed of the biogenesis and activity of two kinds of sRNAs, microRNAs and phased interfering small interfering RNAs. Using a combination of multiple types of NGS datasets and the design of a custom bioinformatics pipeline, a broad scale sRNA-mediated regulatory network was described. Evaluation of the network’s regulatory contribution indicated that sRNA-mediated regulation plays a major role in gene expression. A large proportion of genes in Arabidopsis thaliana were found to be controlled by sRNAs, including genes involved in most biological processes. Finally, the role of sRNAs as key regulators was further confirmed by the extended number of genes under sRNA control that are involved in others aspects of regulation, in particular transcription factors.