Background Root-knot nematodes (Meloidogyne spp.) are among the most important plant pathogens. Biological control is one of the safety and effective methods for control of these nematodes. The aim of the present study was the isolation and identification of endophytic bacteria from tomato fields in some areas of Iran in order to evaluate their biocontrol potential against root-knot nematode. In the present study, the population of Meloidogyne was collected from infected cucumber roots of a greenhouse, and the bacteria were isolated from tomato samples collected from the fields in West-Azarbaijan province of Iran. The effects of the bacterial isolates on hatching and mortality of nematode second-stage juveniles were evaluated, and the effects of six selected isolates on infection of a susceptible cultivar of tomato with nematode were evaluated under greenhouse conditions. Results The root-knot nematode was identified as Meloidogyne incognita. Results showed that the all isolates exhibited considerable inhibitory effects on nematode hatching. The bacterial isolates also caused the mortality of juveniles. Six bacterial isolates with notable biocontrol potential were selected, and supplementary experiments and molecular identification of selected bacterial isolates were performed. Isolates 1, 2, 5, 7, 10, and 11 were identified as follows: Bacillus wiedmannii (MW405861), Pseudoxantomonas mexicana (MW405860), Pseudomonas thivervalensis (MW405862), Serratia liquefaciens (MW405864), Pseudomonas chlororaphis (MW405863), and P. fluorescens (MW405825), respectively. Based on the results of the greenhouse experiment, the selected isolates exhibited good results in terms of reduction of galls and egg masses of nematode. However, B. wiedmannii and S. liquefaciens had the best results in reduction of all investigated factors compared to other isolates. P. mexicana, P. chlororaphis, and P. fluorescens resulted moderate effects. P. thivervalensis was less effective than the others and in some cases had no effect on nematode reduction. Conclusions The results showed that endophytic bacteria are good candidates for management of root-knot nematodes. The use of such agents instead of chemicals will be very valuable to the control of nematodes.