One hundred and fifty endophytic actinomycetes were isolated from three pharmaceutical plants, Annonaceae squamosal, Camptotheca acuminate and Taxus chinensis. Bioactivity test showed that 72.4% of the endophytic actinomycetes displayed inhibition against more than one indicator microorganism. In total, 9.3 and 10.7% showed the cytotoxicity and antioxidant activity, respectively. 3-Amino-5-hydroxybenzoic acid synthase (AHBA), ketosynthase (KS), cytochrome P450 hydroxylases (CYPs) and epoxidase (ES) encoding genes were found in 8.8, 23.8, 2.8 and 11.7% isolates, respectively, by genes screening. The identification based on traditional and molecular methods indicated that diverse genotypes of Streptomyces were distributed in the three pharmaceutical plants, and a few strains of Amycolatopsis were also found in the root of T. chinensis. These results indicated that endophytic actinomycetes associated with pharmaceutical plants could be a promising source of drug leads.