This study attempted to understand pathogenicity of Streptococcus parauberis by comparing genomes of five S. parauberis strains and global gene expression profiling of this pathogen exposed to olive flounder serum. In this study, serotyping of 75 S. paraberis strains was performed. Pathogenicity of 15 strains was evaluated in olive flounder by subcutaneous injection. Whole genome sequencing of three high and two low virulent strains was conducted using PacBio RSII (Pacific Biosciences) single-molecule real-time (SMRT) technology. Total RNA was extracted from samples of S. parauberis SPOF3K cultured in the serum and BHIB (+1% NaCl) for 1, 2 and 4 h. RNA sequencing was performed using Illumina hiseq 2500 platform, and differential gene expression (DEG) was analyzed using Limma/Voom package. As a result, the genome of two strains of serotype Ia contained a 12 Kbp sized plasmid harboring tetracycline resistance and Internalin J gene, known as a virulence factor. Importantly, only serotype Ia strains were found to contain bacterial cellulose synthase, which would be of importance in bacterial biofilm formation and peptidoglycan O-acetyltransferase, which is reported to bring resistance against lysozyme. In our transcriptome analysis, in line with this, these genes were significantly up-regulated. Gene expression profiling showed fifteen important virulence- and nine stress-related genes significantly up-regulated in serum, indicating their crucial role in adapting hostile environment and in pathogenicity. In conclusion, our findings would provide a comprehensive view toward adaptive strategy and pathogenesis of S. parauberis, which would provide fundamental knowledge for further development of control measures in the future.