Beauveria bassiana (Bb) is a potential biopesticide against western flower thrips. To understand molecular characteristics of two Bb isolates (ERL836 and JEF-007), whole genome sequencing and RNA-seq were performed. The whole genome of Bb ERL836 was sequenced (3,934,801,443 bp) using Pacbio sequencing and 15 contigs were analyzed. To understand the molecular mechanisms of pathogenicity in two Bb genome (before infection and after infection), next generation sequencing (NGS) was analyzed to compare transcriptomes. A result of differentially expressed gene (DEG) showed that 2,689 contigs were up-regulated and 2,619 contigs were down-regulated. Randomly selected five genes were validated to be highly up-regulated. This work can provide an understanding of the interaction between Bb and westetn flower thrips.