The endophytes from the wild Noni fruit of Xisha was isolated and identified. Count results showed that the total endophytes' number of mature wild Noni fruit was 1. 0 × 105CFU/g and 8. 0 × 103CFU/g for the endophytic fungi. Furthermore,22 strains of bacteria,14 strains of yeast and 9 strains of mould were isolated. Partial sequence analysis of 16S rDNA,26S rDNA D1/D2 region and ITS rDNA were used for the strains' identification. The results indicated as follows:( 1) 22 strains of bacteria were highly similar to 8 known genus which belong to α-Proteobacteria,β-Proteobacteria, γ-Proteobacteria, Firmicutes and Actinobacteria. The 8 genus were Asaia sp., lavobacterium sp.,Burkholderia sp.,Pantoea sp.,Rhizobium sp.,Paenibacillus sp.,Curtobacterium sp. and Luteibacter sp.;( 2) 14 strains of yeast were highly similar to genus of Cryptococcus sp.,Pseudozyma sp.,Sympodiomycopsis sp. and Eremothecium sp. belonging to Basidiomycota and Ascomycota;( 3) 9 strains of mould were highly similar to genus of Cladosporium sp.,Daldinia sp.,Gibberella sp.,Nemania sp. and Penicillium sp. belonging to Ascomycota. The results showed that there are abundant species diversity of endophytes in the wild Noni fruit of Xisha. The results will lay the foundation for the research and development of functional strain's in Noni.