The number of plant viruses that are known likely remains only a vanishingly small fraction of all extant plant virus species. Consequently, the distribution and population dynamics of plant viruses within even the best-studied ecosystems have only ever been studied for small groups of virus species. Even for the best studied of these groups very little is known about virus diversity at spatial scales ranging from an individual host, through individual local host populations to global host populations. To date, metagenomics studies that have assessed the collective or metagenomes of viruses at the ecosystem scale have revealed many previously unrecognized viral species. More recently, novel geo-referenced metagenomics approaches have been devised that can precisely link individual sequence reads to both the plant hosts from which they were obtained, and the spatial arrangements of these hosts. Besides illuminating the diversity and the distribution of plant viruses at the ecosystem scale, application of these “geometagenomics” approaches has enabled the direct testing of hypotheses relating to the impacts of host diversity, host spatial variations and environmental conditions on plant virus diversity and prevalence. Specifically, in the single geometagenomics study so far published, the detected proportion of infected plant samples (a proxy for virus prevalence) was higher for cultivated host plants than for uncultivated ones. Likewise, it was found that overall virus prevalence was generally higher in cultivated crop areas than in natural vegetation areas. These findings indicated that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.