[Objective] To isolate endophytic actinomycetes from Dongxiang wild rice (Oryza rufipogon), and to study the classification, antimicrobial activity and analysis the secondary metabolites from the high active strain S123. [Methods] S medium was used to isolate endophytic actinomycetes from Dongxiang wild rice. The isolates were classified by 16S rRNA gene sequence analysis. Antimicrobial activity of the isolates was tested using agar diffusion and growth rate method. Meanwile, to screen the potential activity compounds, The degenerated primer targeted on type-I polyketide synthase (PKS-I) was designed. Bioactivity strain S123 was subjected to large scale fermentation for isolating secondary metabolites. The compounds were separated and purified by various chromatographic methods, and the structure was determined by mass spectrum and nuclear magnetic resonance analyses. [Results] We obtained 11 actinomycete isolates from Dongxiang wild rice. The isolates belonged to 2 genera, Streptomyces (8) and Pseudonocardia (3). Among of these isolates 8 strains show their anti-microbial activities and 8 strains were positive for type-I PKS genes. Two compounds were isolated from strain S123 and determined as Nigericin and 17-O-demethylgeldanamycin separately. The compound Nigericin showed inhibition against Staphylococcus aureus, Bacillus subtilis and Rhizoctonia solani. [Conclusion] This is the first report of endophytic actinomycetes from Dongxiang wild rice and identified two activity compounds Nigericin and 17-O-demethylgeldanamycin associated with type-I PKS genes. It provides a reliable basis for studying Dongxiang wild rice endophytic actinomycetes diversity and seeking activity secondary metabolites.