Endophytic nitrogen-fixing bacteria were isolated from roots,stems and leaves of rice Chujing27 collected in Lufeng County of Yunnan Province and its inhibition was identified.125 isolates were obtained by nitrogen-free medium and 15 strains were identified as nitrogen-fixers with PCR amplification of nifH gene fragments.Endophytic bacteria in different parts had different density,with peak value in roots and the lowest density in stems.Among the 125 isolates,11 endogenetic strains had suppressive effect on five main bacteria diseases, Xanthomonas oryzae pv．oryzae,Xanthomonas oryzae pv．oryzicola，Pyricularia oryzae Cav.，Thanatephorus cucumeris (Frank) Donk，Fusarium moniliforme Sheld.of rice.Three strains (NR-18,NR-64 and NR-79) isolated from roots had both functions.16S rDNA sequence analysis showed that NR-18 and NR-79 were identified as Paenibacillus polymyxa and NR-64 was identified as B．subtilis.The experiment above showed that the 3 nitrogen-fixing bacteria isolated and identified had potential value on agriculture.It was the first time that Paenibacillus polymyxa isolated as nitrogen-fixing bacteria had antipathogenic functions in the root of rice.