Black pepper is an industrial crop with high economic and export value. However, black pepper production in Vietnam has been seriously affected by the root-knot nematodes, Meloidogyne spp. The purpose of this study was to select active endophytic bacteria (EB) for the cost-effective and environmentally friendly management of Meloidogyne sp. Thirty-four EB strains were isolated. Of these, five isolates displayed the highest activity, demonstrating 100% mortality of J2 nematodes. These active EB were identified based on sequencing and phylogenetic analysis of the 16S rRNA gene; notably, all the potential endophytic bacterial strains belong to the genus of Bacillus. In greenhouse tests, Bacillus megaterium DS9 significantly reduced nematodes in the soil and pepper plant roots with great inhibition values of 81.86% and 73.11%, respectively, with the lowest rate of nematodes built up at 0.23. This active antinematodes strain also showed good effect on promoting pepper plant growth. Some enzymatic activities, including chitinase and protease activity related to the biocontrol of Meiloidogyne sp., were also detected. The results investigated in the current study suggested that these selected EB strains may be good candidates for biocontrol agents of Meloidogyne sp., and plant promoting effects. The results also enhanced the novel active antinematode endophytic bacterial communities.