Abstract: The metagenome of ecosystem of endophytic bacteria associated with the pine wood nematode Bursaphelenchus xylophilus was analyzed by 16S rRNA gene library and illumina Miseq sequencing. The results showed that the dominant bacteria were Xanthomonadaceae (22.41%), Sphingobacteriaceae (17.66%), Comamonadaceae (14.71%) and Rhizobiaceae (10.17%). Five endophytic bacteria were isolated from B. xylophilus using dilution plate method. These bacteria were classified by phenotypic and genotypic characteristics. The five endophytic bacteria all showed nematocidal activities in vitro. The bacterium Klebsiella sp. sct5 showed highest nematocidal activity, and 100% of the tested B. xylophilus were killed within 4 days. Furthermore, the strain sct5 could produce proteases and form biofilm quickly in vitro. Moreover, the bacterial strain sct5 had compatible relationship with Bacillus nematocida B16. The compatible combination of sct5 with B16 resulted in enhanced nematocidal activities within 1 d (75％) against Bursaphelenchus xylophilus as compared to the single strain sct5 (60％) or B16 (40％). In contrast, the incompatible combination of sct29 with B16 led to reduced disease nematocidal activities (only 13％ within 1 d). This study firstly reported nematocidal activities of endophytic bacteria isolated from Bursaphelenchus xylophilus and their relationships with pathogenic bacteria Bacillus nematocida B16, which lays theoretical foundations for developing co-inoculated bacterial strains in biocontrol and improving the stability of bio-control strains. Also, our research explains the relationships between endophytic bacteria in Bursaphelenchus xylophilus and pathogenic bacteria from a new perspective.