Abstract: The endophytic fungus Shiraia sp. Slf14 is a strain that can produce huperzine A and bambusin A, which is isolated from Huperzia serrata. To understand the genetic characteristics of Shiraia sp. Slf14, we performed whole genome sequencing of the strain. The whole genome of Shiraia sp. Slf14 was sequenced and analyzed based on the second-generation sequencing technology. Quality control and assembly, functional annotation, comparative genomic analysis, phylogenetic analysis and secondary metabolites analysis were performed by bioinformatics software. The genome size of Shiraia sp. Slf14 was 32 067 383 bp, the N50 value was 525 954 bp, and the G+C content was 47.96%. The genome was predicted to contain 11 242 CDS, the total tRNA was 106 and the total rRNA was 27. 3 822, 3 223, 8 837 and 563 genes were annotated in GO, KEGG, KOG and CAZY, respectively. Phylogenetic results show that the endophytic fungus Shiraia sp. Slf14 belongs to the genus Shiraia. Prediction results indicate that there are 50 secondary metabolite synthesis gene clusters in the endophytic fungus Shiraia sp. Slf14, which possess the potential to synthesize a variety of bioactive substances, including RiPP, T1PKS and NRPS. Furthermore, gene clusters potentially involved in the biosynthesis of huperzine A and hypocrellin A were also predicted.