[Objective] We studied secondary metabolites of endophytic Micromonospora sp. M66 of Tripterygium wilfordii Hook. f., a rare actinomycete, provide structurally diverse compounds for microbial drugs and pesticides development. [Methods] Combining thin-layer chromatography, silica gel column chromatography, gel chromatography and semi-preparative high-performance liquid chromatography, we purified the secondary metabolites from Micromonospora sp. M66. By using the spectroscopic techniques, we elucidated their chemical structures. [Results] Seven compounds were purified and their chemical structures were elucidated through spectroscopic analysis including mass spectroscopies and nuclear magnetic resonance (NMR) spectroscopies. These 7 compounds were a set of indole alkaloids derived from tryptophan or indole. Compound 2 was an important plant growth regulator. Compound 3 showed a notable growth inhibition of lymphocytic leukemia cell P388, Bacillus subtillis and Saccharomyces cerevisiae, whereas compound 6 exhibited a significant inhibiting activity against Staphylococcus aureus. [Conclusion] Compounds from the bacteria of the genus of Micromonospora produce indole alkaloid-like secondary metabolites by using indole or tryptophan as a starting material and have potential as new alkaloid-like drugs.