Community assembly of diverse mutualistic symbionts in host plants have recently received much attention. On the other hand, for decades, researchers have also focused on a role of genetic variation for shaping ecological communities. However, it remains unclear how local interaction networks between a host and symbionts are shaped from the pool of genetically diverse microorganisms in the natural rhizosphere. In this study, we comprehensively analyzed local and regional genetic communities of Frankia in host individuals and in surrounding soils using metabarcoding to unravel community assembly in shaping interaction networks between plants and root nodule symbionts, both of which are genetically diverse, in natural ecosystems. We found that Frankia communities in rhizosphere soil were consisted of tremendously diverse strains. The diverse Frankia communities in rhizosphere soils were heterogeneously structured by the presence of host individuals and soil nutritional status. Furthermore, quantification of the filtering forces by community analysis demonstrated that the filtering forces that shape symbiotic networks would depend on genetic variation in the host plant. This study suggests that filtering mechanisms and host genetics would have a profound role in shaping plant-bacterium symbiotic networks in natural environments.