Pine trees are ecologically important in Korea. They are seriously imperiled by Pine wilt disease (PWD), by pine wood nematode (PWN, Bursaphelenchus xylophilus). Here, we isolated and characterized bacterial endophytes (BEs) from pine trees in Korea for biological control of PWN using BE metabolites. Using culture-dependent approach BE isolates were extracted from three tissues (needles, stems, and roots) of four pine species across 18 sampling sites in Korea. Bacterial isolates were characterized into 389 distinct isolates based on 16S rDNA sequencing. Ethyl acetate crude extracts (CEs) of bacterial liquid cultures were prepared using ethyl acetate and screened for nematicidal activity against PWN. BEs (1,622 isolates) were isolated; their taxonomic binning resulted in 215 operational taxonomic units (OTUs). Analysis of species richness and Shannon’s diversity of the three tissues revealed that BEs colonized the needles more than the stem and root tissues. Furthermore, based on nematicidal activity screening of 389 isolates, 44 BEs were identified, with two isolates exhibiting a significant inhibitory activity against PWN. Taken together, these data revealed numerous nematicidal BEs in pine trees, providing new insights that can serve as an effective and promising alternative approach to combat PWD.