[Objective] In order to explore new potential agricultural biocontrol actinobacteria strains and discover drug lead compounds, the diversity of endophytic actinobacteria isolated from medicinal Melia toosendan Sieb. et Zucc. were researched. [Methods] 148 endophytic actinobacteria were isolated from Melia toosendan Sieb. et Zucc. collected in Ziyang, Suining of Sichuan Province and Chongqing by four isolation medium. Based on morphological characteristic, 60 isolates were selected and analyzed by 16S rRNA-RFLP, the representative strains were further sequenced. Antibacterial activity of 60 strains were evaluated by three bacteria and six pathogenic fungi strains, respectively, and the genes coding for polyketide synthases (PKSI, PKSII), nonribosomal peptide synthetase (NRPS) and halogenated enzyme gene (Halo) were amplified. [Results] 60 strains of actinobacteria were divided into 10 clusters based on 16S rRNA-RFLP analysis, 25 strains of representative strains belonging to 7 genera: Streptomyces, Micromonospora, Planotetraspora, Streptosporangium, Nocardiopsis, Prauseria, Microbispora, the genus Streptomyces accounted for 73.3%. An evaluation of antimicrobial activity showed most isolates possessed activity towards pathogenic bacteria and fungi. The frequency of PCR amplification of 4 synthesis genes was 10%?55%. [Conclusion] This study indicated that endophytic actinobacteria associated Melia toosendan Sieb. et Zucc. are abundant and the distribution is influenced by sampling sites and plant organs, which possessed potential diverse bioactivities and can be further explored.