To explore the diversity of species and biological activities of the endophytes from Huperzia serrata that is a wild medicinal plant under state protection (category ii), and to discover and collect endophytic bacteria from medicinal plants.Huperzia serrata samples were collected from Sichuan and Fujian Provinces. Culture-dependent method was used to obtain endophytes from the surface-sterilized plant samples. The diversity of the isolates was analyzed according to the 16S rRNA gene sequences information. Jaccard index, Shannon-wiener Index, Simpson Index and Pielou Index were calculated. Then six screening models were followed to study the physiological activities of the isolates, based on which we evaluated the diversity of biological activities of the endophytes from Huperzia serrata and their potential medicinal value.A total of 356 endophytic bacteria were purified from Huperzia serrata, and the analysis results of their 16S rRNA gene sequences showed that they affiliated to 41 genera of 26 families in the phyla Actinobacteria, Firmicutes and Proteobacteria. The numbers and biodiversity indexes of endophytes from the aboveground part and belowground part of Huperzia serrata were approximately equivalent. Among them 11 potential novel species belonged to the genera Amycolatopsis, Angustibacter, Arthrobacter, Curtobacterium, Frondihabitans, Glaciihabitans, Jatrophihabitans, Luteimicrobium, Massilia, Naumannella and Tardiphaga, and 1 novel genus of the family Dermacoccaceae was discovered. The screening for anti-microbial results from these 356 isolates were as follows: the activity rates of against Enterococcus faecalis, Klebsiella pneumonia, Mycobacterium smegmatis and Xanthomonas campestris were 9.0%, 1.4%, 2.2% and 0.8% respectively. Of them 4.5% exhibited activities on the screening model of statins-like antihyperlipidemics showing inhibition of Sporobolomyces salmonicolor SS04; 8.6% of them had the activities of against HIV-1. In total, the fermentation broths from 74 strains exhibited activities on at least one screening model, the positive rate among the isolates was 20.8%.This study demonstrated that the endophytic bacteria from Huperzia serrata were of great significant bio-diversity and antibiotic diversity, therefore, they could be an ideal microbial resource for further discovery of new natural products.