The alpine meadow in the Qinghai-Tibet Plateau is the main natural pasture in China, and it is also an important ecosystem and alpine plant gene bank. The dominant meadow plants which show strong adaptions to the alpine climate are of great significance to grassland animal husbandry and maintenance of alpine ecosystem functions. Plant endophytes can promote plant growth because of their participations in nutrient cycling, hormone production as well as suppression of pathogens. Diverse and abundant endophytes harbored within leaf and root as symbioses with their hosts are critical to hosts' survival. Exploring community structure and diversity of prokaryotic communities, especially the endophytes of dominant plants in alpine meadows could provide new insights into the interactions between plants and their symbionts in the alpine environments. Bulk soil surrounding plants is a ‘seed pool’ of the microbes for plants, affecting the recruitment of the endophytes. However, the differentiations of prokaryotic communities among root endosphere, leaf endosphere and bulk soil in compositions and community structure need to be further explored. Here, we collected three dominant plants in alpine meadows including Carex moorcroftii, Leontopodium jacotianum and Carex vulpara, to study prokaryotic community compositions in leaf endosphere, root endosphere and bulk soil, and how sample types and plant types contributed to the variations of microbiomes using amplicon sequencing of 16S rRNA genes with Illumina HiSeq platform. The results showed that: 1) At phylum level, 13 phyla were significantly different among leaf endosphere, root endosphere and bulk soils (P<0.05), and only 5 phyla, namely Proteobacteria, Firmicutes, Acidobacteria, FBP and Verrucomicrobia, were statistically different among three studied plants (P<0.05). 2) For alpha diversity, there were significant differences among different sample types in all three plants (P<0.05), while significant differences of alpha diversity among different plants (P<0.05) were only observed in root endosphere and soil communities, and no significant differences were observed in leaf endosphere (P>0.05). 3) Sample type was the most important factor determining the structure of prokaryotic community, contributing 20.13% to the variation of prokaryotic community structure. The prokaryotic community structure among different plants also had significantly differences, and plant types contributed 14.41% to the total variation. The strong interactions between plant types and sample types were also observed (17.40%). The results indicated that leaf endosphere, root endosphere and bulk soil created unique niches for prokaryotic communities, showing microbial niche differentiations with sample types and plant species and reflecting certain adaptability of prokaryotic communities to these niches. Finally, we identified the specific microbes in leaf endosphere and root endosphere which were significantly different from those in soils. Pseudomonas, as a typical representative, was significantly enriched in both leaf endosphere and root endosphere. These microbes contained functional genes involved in various metabolic processes and had important potential functions in promoting nutrient uptake and improving plant ecological adaptability in cold environment. This study revealed key factors driving the differentiations of prokaryotic communities in dominant alpine meadow plants, and the plant-endophyte interactions in different plant compartments.