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The root-knot nematode (Meloidogyne spp.), which represents a global threat to agricultural production, can cause serious losses in both the yield and quality of many crops. Endophytic bacteria are known to have great potential against Meloidogyne incognita. The colonisation ability of endophytic Bacillus cereus BCM2 in tomato roots and its biological control efficacy of M. incognita were investigated. By the end of the growth period of tomato plants, the population of BCM2 in the rhizosphere soils and roots of the tomato were 5.86 and 3.38 log CFU g−1, respectively, indicating that BCM2 can colonise tomato roots for long periods of time. Pre-inoculation with BCM2 resulted in a significant reduction in the population of M. incognita and the gall index of tomato compared to the untreated control, and there was an increase in the tomato yield of 47.4%. Colony counts showed that the population of BCM2 in tomato roots was affected by soil type and pH, and the colonisation of BCM2 in tomato rhizosphere soils was influenced by soil water and organic matter contents. We observed that the biocontrol effects of BCM2 were best when soil pH was 7. Pre-inoculation with BCM2 can inhibit the formation of tomato galls more effectively when soil water content is 25%, and rich organic matter content was conducive to a reduction in the number of M. incognita second stage juveniles (J2s) in soil. These results demonstrated that B. cereus BCM2 has great potential for controlling M. incognita in tomato plants. [ABSTRACT FROM AUTHOR]