Background: The grasses in adverse environment such as Qinghai-Tibet Plateau are hypothesized to survive the harsh climate in part upon their seed-borne microorganisms, and yet the characteristics of the grass seed microbial communities remain undetermined. Here, we assessed the seed microbial communities of three native gramineous grass species (Avena sativa, Elymus sibiricus and Elymus dahuricus) and four candidate legumes (Vicia villosa, Trifolium repens, Trifolium pretense and Medicago sativa) on the Qinghai-Tibet Plateau by high-throughput sequencing. Results: A total of 1,013 bacterial operational taxonomic units (OTUs) and 922 fungal OTUs were observed. The OTUs that shared in all the samples were in high abundance but with different relative abundances. The majority of bacterial sequences were assigned to Proteobacteria (54~90%) and Firmicutes (5~41%), and the fungal communities were mainly composed of Ascomycota (23~96%) and Basidiomycota (2~11%). The fungal communities were more affected by host genetic distance than bacteria. The three gramineous grasses were speculated to survive the adversity partly due to their high abundance of beneficial bacteria like Pantoea or Bacillus, and non-pathogenic fungi like Candida or unclassified Helotiaceae. Also enriched with these potential beneficial taxa, the four leguminous grasses may be competent to adapt the Qinghai-Tibet Plateau stress. Furthermore, the higher tolerance grasses (Elymus sibiricus and Elymus dahuricus) possessed a greater number of growth-promoting and tolerance bacterial and non-pathogenic fungi. Conversely, the less tolerance grass Medicago sativa contained lower levels of such microorganisms, and showed higher abundance of pathogenic taxa. Furthermore, the isolated Bacillus subtilis or Pantoea agglomerans could more probably promote seeding growth of hosts with lower abundance of them, while inhibit if the endo-abundance of was high. Conclusions: Seed-resident microbiome structure of the four cold-tolerance legumes and three Qinghai-Tibet Plateau gramineae is host dependent and related to stress resistance. It also has a strong influence on the response of seedlings to biological seed treatments. This study provides valuable data for studying plant resilience, identifying more biocontrol strains, maximizing microbial functions in ‘smart farming’ practices.