The community structure and diversity of endophytic bacteria in the fruit of Xisa Noni growing in Hainan yongxing island was investigated using the 16S rDNA clone library technique for the first time. It was the first time that Mothur software was applied to analyze the obtained data and a Mothur software data analysis platform was established. The results showed that 93clones were grouped to 12operational taxonomic units and most of the clones showed high similarity to the known cultured bacteria. Sequence analysis revealed that three phyla of bacteria were identified in the 16S rDNA library and alpha, beta and gamma subclasses of the Proteobacteria,Actinobacteria and Firmicutes were involved. The dominant endophytic bacteria group of the Noni fruit belonged to Piscinibacter genera. The dominant bacterium was Piscinibacter sp.(80.65%), Streptococcus sp.(3.23%), and Methylobacterium sp.(2.15%). The result demonstrated that abundant endophytic bacterial resources were existed in the fruit of Xisa Noni from Hainan yongxing island and further researches could be developed based on the results of this project.