Abstract: Oryza rufipogon that possess abundant habitat, genetic and microbial diversity is a valuable wild rice resource. The collection of endophytic bacterial strain resources from O. rufipogon could be used for micro-ecosystem research and application in agricultural fertilizer production. In this study, a total of 111 endophytic bacterial strains were isolated from O. rufipogon in Yuanjiang, Yunnan Province, including 82 phosphorus solubilizing bacteria, 23 nitrogen-fixing bacteria, 50 siderophore-producing bacteria and 18 indole-3-acetic acid (IAA)-producing bacteria strains. Strains of Bacillus subtilis ORS2-5 and Enterobacter ludwigii ORS1-2 were isolated from stem tissues, and Kosakonia oryzae ORL3-1 was isolated from leaf tissues, showing the highest IAA productivity with yields of 11.69, 22.81 mg/L and 24.62 mg/L. The greenhouse experiment showed that these strains significantly promoted perennial rice growth. Our study indicated that endophytic bacterial strains isolated from O. rufipogon have great potential to be developed as microbial fertilizers for perennial rice, which will meet the simplified cultivation model of perennial rice.