A large number of sphyraenus bred in the Qiantang River reservoir of Zhejiang province died in 2013 and 2014 and the death rate reaches 40%. The diseased sphyraenus features exophthalmos and Intestinal hyperemia. To find the pathogen and avoid this disease, this paper studies the bacterial strain MSB0507 separated from the brain and liver of the sphyraenus. After animal regression test, the bacterial strain MSB0507 is identified as the pathogenic bacteria. After the bacterial strain morphology and bio-chemical identification, the streptococcus dysgalactiae is identified roughly as the disease-incurred bacteria. With 16S rDNA detection, PCR resultant sequencing and ribotide sequence comparison and retrieval, it is found that the homology of the streptococcus dysgalactiae with NCBI registration number AB537922 reaches 100%. The special prime is designed according to the surface protein MIG gene sequence of the streptococcus dysgalactiae and then the target section is grown smoothly. From the view of the molecular biology, this bacterium is identified as the streptococcus dysgalactiae. The medicine sensitivity test results indicate that this separated bacterial strain is sensitive to the antibiotic such as achromycin and soil enzyme. This paper proves that the streptococcus dysgalactiae incurs the disease of the sphyraenus and guides diagnosis and treatment of this disease.