To seek the community composition and differential of endophytic bacteria and fungi in different dormancy states of Notopterygium incisum Ting ex H.T.Chang.seeds,the amplified fragments of 16S V5+V7 region and ITS1-IF region in N. incisum seeds from different dormancy states ［morphological and physiological dormancy state (GSA),morphological dormancy release state (GSB),physiological dormancy release state (GSC)］ were sequenced by Illumina Miseq high-throughput sequencing technique,associating with bioinformatics assay to analyze.The results showed that the diversity of endophytic bacteria was higher than the fungi.The types of endophyte community composition were similar at the phylum level,but abundance exhibited significant difference in different dormancy states.The types of endophyte community composition were changed from GSA to GSB at the genus level,were similar from GSB to GSC and abundance exhibited significant difference.The community diversity of endophytic bacteria increased significantly from GSA to GSB,and then no significant difference to GSC by Alpha diversity analysis,the community diversity of endophytic fungi have no significant difference during the entire dormancy release process.The community structure of endophytic bacteria exhibited significant difference among GSA,GSB and GSC,the community structure of endophytic fungi changed significantly from GSA to GSB,and then no significant difference to GSC.LEfSe analysis showed that there are 37 differential taxonomic branches of endophytic bacteria (a=0.01,LDA≥2.0),but none for endophytic fungi.This study identified the community composition and differential of endophytic in different dormancy stages of N. incisum seeds,and enrichd the resources of endophytic bacterial and fungi,have instructional significance for further study using microbial methods to promote dormancy release of N. incisum seeds.