In this study two Bacillus pumilus including ToIrFT- KC806241 and ToIrMA-KC806242 were obtained from tomato fields and characterized based on phenotypic and molecular properties. Their possibility to reduce root knot disease of tomato caused by Meloidogyne javanica was evaluated. The experiments were done in lab and under pot conditions. Application of the ToIr-MA against M. javanica reduced the number of galls and eggs. Preliminary results indicated that the ToIr-MA has an ability to produce proteolytic enzymes in lab conditions. It seems that the bacterial culture filtrates can suppress egg hatching and increase juvenile's mortality, but the role of these metabolites in disease suppression needs to be investigated. Significant enhancement in root and shoot length (33%) and dry root and shoot weight (64 and 67%) was also recorded over usage of strain ToIr-MA in comparison to untreated controls. Additionally, survival of bacterial strains in rhizosphere and increases in population density were seen using root colonization assay. To our knowledge, this is the first time that such B. pumilus strain with nematicidal activity against M. javanica has been reported in Iran which may suggest to manage disease and change microbial population dynamics in the rhizosphere.