[Background] People tend to study endophytic actinomycetes to discover new compounds due to the increasing difficulty to obtain new compounds from soil actinomycetes and antibiotic abuse causing increased resistance of pathogens. [Objective] We explored the diversity of endophytic actinomycetes isolated from toxic plants in Xishuangbanna tropical rainforest, and isolated strains with antibacterial potential to develop new drugs. [Methods] We analyzed communities of endophytic actinomycetes from three toxic plants, Antiaris toxicaria Lesch., Alangiumchinense (Lour.) Harms and Lantana camara L. by Illumina HiSeq high-throughput sequencing and culture-dependent approach. Antimicrobial activity was screened by disk diffusion test and seven synthetic genes were detected by PCR amplifications. [Results] Strains from 3 toxic plants were identified at the phylum level with 2 phyla of the Archaea, 18 phyla and the tentative RsaHF231, WD272 of the bacteria. And 30 genera of actinomycetes were detected at the genus level. Both the microbial community structure of Alangiumchinense (Lour.) Harms and Lantana camara L. were more abundant than Antiaris toxicaria Lesch. In total 34 strains of 11 genera were isolated from culture-dependent approach. Most of the genus detected by high-throughput could not be obtained through pure culture. The antibacterial activity results showed that Streptomyces had broad spectrum antimicrobial activity. The detection rates of NRPS and PKS in Streptomyces were significantly higher than other compounds synthetic gene. [Conclusion] The diversity of endophytic actinomycetes in toxic plants is very rich. Actinomycetes in the toxic plants secondary metabolites synthesis have enormous potential to provide an abundant microbial resource for the development of biological pesticides and antibiotics.