With the attempt to address the knowledge gap and preliminary clarify the dynamic molecular responses of Strongylocentrotus intermedius to pathogen infection, we performed a serial of transcriptome sequencing to explore the dynamic gene (mRNA) expression profiles in S. intermedius during 0 to 96 h post-infected by a causative pathogen strain of sea urchin black peristomial membrane disease (Vibrio sp. strain SIBMPM02).