Objective  Being crucial to the development of rhizobium inoculants and the understanding on the associated mechanisms of soil nitrogen fixation, community structure of the endophytic microorganisms in root nodules of Astragalus sinicus L. was investigated.

  Method  Endophytic microbial community in the root nodules of 7 cultivars of A. sinicus planted in Fujian was analyzed with the Illumina Miseq PE300 sequencing platform using 16S rRNA as the target gene.

  Result  The microbial composition of endophytic community in the nodules of the different cultivars varied. For instance, the predominant genus in ZZ5 root nodules was Pseudomonas, but it was Mesorhizobium in other cultivars. Furthermore, high Shannon indices were found in the root nodules of MZ8, XY, and ZZ5 with diverse non-rhizobial endophytes like Pseudomonas, Stenotrophomonas, Duganella, Erwinia, etc. In contrast, high relative abundances of pathogens, such as Erwinia rhapontici and Pantoea ananatis PA13 existed in the root nodules of MZ8, XY, and ZZ5.

  Conclusions  Significant microbial variations in the endophytic communities were evident among the different varieties of A. sinicus planted in Fujian. The predominant genus in the root nodules of ZZ5 was non-rhizobial, growth-promoting Pesudomonas, while it was rhizobia for the other cultivars.