Abstract: The endophytic nitrogen-fixing bacteria could transform the nitrogen in the air into ammonia nitrogen available for the plants through their own nitrogen fixation, thus to promote the plant growth and increase the crop yield. By using the tomato root tissue infected with the root-knot nematode as the material, the endophytic bacteria in tomato roots were isolated and purified by the methods of gradient dilution and streaking. The nitrogen fixing bacteria were screened by the continuous culture in the nitrogen-free solid medium. Then, the 16S rRNA gene sequence of nitrogen-fixing bacteria was amplified for the identification and phylogenetic analysis, thus to explore the species and distribution of endophytic nitrogen-fixing bacteria in tomato roots infected with the root-knot nematode. The results showed that the three endophytic strains with stable nitrogen fixation ability were obtained after continuously subculturing the selected and purified 33 strains of endophytic bacteria in tomato roots in the nitrogen-free culture-medium. The molecular identification and sequence analysis showed that there were 8 strains of Bacillus, 1 strain of Xanthomonas and 1 strain of Rhizobium in the selected strains of endophytic nitrogen-fixing bacteria. The cluster analysis of the dominant OTU of endophytic bacteria in tomato roots previously published indicated that Rhizobium was the dominant population of endophytic nitrogen-fixing bacteria in tomato roots infected with the root-knot nematode.