Abstract: 【Objective】The community structure and diversity of endophyte in different tissues of Angelica keiskei （Miq.）Koidz. was analyzed，to provide a theoretical basis to explore the interaction mechanism and functional strain screening of A. keiskei and endophyte.【Method】 The medicinal and edible plant A. keiskei，which was cultivated in Yibin， Sichuan，was taken as the object. The diversity of endophytic fungi and bacteria in the root，stem，leave and fruit tissues was examined by high-throughput sequencing using Illumina MiSeq.【Result】According to the 97% sequence similarity， endophytic fungal and endophytic bacterial reads could be indentified into 1023 and 1871 operational taxonomic units （OTU），respectively. A Venn diagram and a heatmap showed that there were fairly high community structure difference between endophytic fungi or endophytic bacteria in the four different parts of tissues of A. keiskei，and the abundances of populations differed. According to α diversity analysis，the variety of endophytic fungi in the leaves of A. keiskei was the most，the diversity of endophytic fungal community in the roots was the lowest，and the abundance of endophytic fungal community in the fruits was the lowest. The variety of endophytic bacteria in the roots of A. keiskei was the most，the diversity of endophytic bacterial community in the stems was the lowest，and the abundance of endophytic bacterial community in the fruits was the lowest. β diversity analysis showed that the characteristics of tissues had a significant effect on the community structure of the endophytic fungi or endophytic bacteria in A. keiskei. Ascomycota and Proteobacteria were the dominant fungal phylum and bacterial phylum in the four different parts of tissues of A. keiskei respectively. The dominant genera of endophytic fungi in the roots，stems，leaves and fruits were Serendipita，Paramycosphaerella，Trichomerium and Apiotrichum respectively，and the dominant genera of endophytic bacteria were Ralstonia，Methylobacterium and Vibrio respectively. Linear discriminant analysis showed that，the most important biomarkers of the endophytic fungi in the stems，leaves and fruits were Paramycosphaerella，Pallidocercospora and Strelitziana respectively. The most important biomarkers of endophytic bacteria in stems，leaves and fruits were Ralstonia，Methylobacterium and Leucobacter respectively. FUNGuild and COG functional predictions showed that the function of endophyte in different tissues was abundant，and there was a large proportion of unknown functional endophyte in addition to those that could fix nitrogen， promote growth and inhibit bacteria.【Conclusion】 There are abundant and diverse endophytes in A. keiskei. The community structure，diversity，dominant genera and biomarkers in different tissues are conservative and different，and the difference of tissue characteristics is an important factor affecting the endophyte. The ecological functions of endophyte in different tissues are also quite different，and a large number of species and functional endophyte are not identified.