Aims: To characterize the nematicidal endophytic bacteria (NEB) of Wasabia japonica (wasabi) and evaluated the control efficacies of promising NEB as well as fresh wasabi residue (FWR) against Meloidogyne incognita on tomato. Methods and Results: By in vitro bioassay, 53 NEB strains showing nematicidal efficacies of > 50% against J2 of M. incognita were isolated from wasabi. Basing on 16S rRNA gene sequences, these NEB were identified into 18 species of 11 genera. In greenhouse, incorporation of selected NEB culture or FWR into potted soil significantly reduced infection of M. incognita on tomato. Treating tomatoes with either FWR or NEB of Raoultella terrigena RN16 and Pseudomonas reinekei SN21 in the field yielded excellent control efficacies against M. incognita, especially the combinations of FWR with either R. terrigena RN16 or Ps. reinekei SN21 at doses of 50 g plus 100 ml per plant or more. Conclusions: The results established that R. terrigena RN16 and Ps. reinekei SN21 applied separately or combined with FWR have the potential to provide bioprotection agents against M. incognita. Significance and Impact of the Study: This study provides novel way for disease management using combination of endophyte and host residue.