[Aim] Verticillium lecanii is a well-known biocontrol agent of fungal phytopathogens as well as insect pests. It is important to investigate the molecular basis of the pathogenicity.[Method] We analyzed the transcriptome of V. lecanii isolated from Boettcherisca peregrina.[Result] A total of 1634670 high-quality reads were produced by RNA-seq method with Q20 percentage of 89.47% and the GC percentage of 48.50%. The Nr, Swiss-Prot, Gene Ontology (GO), Clusters of Orthologous Group (COG), and Kyoto Encyclopedia of Genesand Genomes (KEGG) databases were used to annotate unigenes functions. Of the 14856 Unigenes assembled, 1467, 9379, 6518, and 4188 were mapped by Nr, Swiss-Prot, COG, and KEGG, respectively. In the GO database, 21403 Unigenes were classified into 38 functional groups, belonging to three main categories:cellular components (1369), molecular functions (1679), and biological processes (1928). Based on COG annotation, 6518 Unigenes were classified into 24 functional categories. The important functional groups identified via GO and COG enrichment were responsible for general function prediction only, secondary metabolites biosynthesis, transport and catabolism, and signal transduction mechanisms. Unigenes mapped to 108 KEGG pathways, most of which were associated with metabolic pathways and biosynthesis of secondary metabolites.[Conclusion] Our results will be helpful to find the pathogenic factors of V. lecanii and enrich its pathogenic mechanism.