Insects are the dominant animals in the world, with more than one million described species. Insects, not only produce direct damage to plants but also acts as a vector for various pathogens. In recent years, next-generation sequencing (NGS) techniques have provided fascinating opportunities to understand the basic biology, biochemistry, and molecular biology of these intimate and intriguing relationships. The decrease in sequencing costs and extensive sequencing services from NGS providers has brought many scientists to be involved in genome sequencing of insects and their associated entomopathogens. By using high-throughput genomic technologies, scientists can elucidate the virulence, host adaptation and gene function of the particular entomopathogen including virus, fungi, bacteria and nematode.