Plant microbial communities may moderate the plant responses to different abiotic or biotic stresses like pathogens. On the other hand, plant genotypes may influence the composition and structure of the plant microbiota. In the Chinese Yuanyang terraces (YYT), a sustainable rice disease control has been achieved for centuries using mixtures of traditional genetically diverse rice varieties harboring a wide panel of resistance genes. However, this centuries-old agrosystem is currently challenged by the introduction of several “modern” rice varieties. The potential simplification of the rice varietal landscape is likely to drive a modification of the rice microbiota, which may have an impact on the plant-pathogen dynamics, and further on the frequency, extent and impact of disease emergence events. We here investigated the microbial communities (bacteria, fungi and viruses) associated with roots and aerial organs from eleven and eight YYT fields cultivated with traditional and “modern” rice varieties, respectively. Besides using a genotyping-by-sequencing approach (GBS) to decipher the rice genetic diversity, microbial communities were characterized by metagenomics approaches. The GBS approach confirms a shift of the rice genetic diversity and split the varieties into three lineages (traditional varieties, “modern” introduced varieties and one Japonica traditional variety). Metagenomics approaches show that microbial communities from aerial organs are lineage-dependent and that microbial communities from the roots are more homogeneous and not different among rice lineages. Interestingly, our study reveals a high prevalence (15%) of Southern rice black-streaked dwarf virus in Yuanyang terraces, and that this virus is significantly more prevalent in traditional local varieties.