Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease and rainbow trout fry syndrome, is currently an important pathogen causing great economic loss to the salmonid industry worldwide. Recently, the genomic evolution and pathogenic mechanisms of F. psychrophilum have been widely studied in many countries. However, these studies that originated from China are still rarely reported. In order to better understand the genomic evolution and pathogenesis of F. psychrophilum in China, the virulent strain CH06 was subjected to whole genome sequencing and analyzed using comparative genomics, and virulence-associated genes were predicted. The result of whole genome sequencing showed that the CH06 genome consists of a single circular chromosome of 2 836 981 base pairs (bp) harboring 2 437 protein-coding genes with an overall G+C content of 32.56%. The results of ANI analysis showed that ANI values between CH06 and 12 F. psychrophilum strains are higher than 99%, indicating that CH06 belongs to F. psychrophilum. Analysis of the genome sequence reveals that CH06 consists of 5 insertion sequences, 4 genomic islands and 3 prophage sequences, indicating that these mobile genetic elements led to the genome evolution of CH06. Collinear and phylogenetic analysis showed that CH06 is more closely related to CSF259-93 and FPG101. Secretion system analysis showed that CH06 carried type I (T1SS) and type IX (T9SS) secretion system. Among the coding proteins, 56 proteins are predicted to be secreted by the T9SS. Furthermore, CH06 was predicted to encode 11 histidine kinases (HKs) and 16 response regulators (RRs), revealing that CH06 has evolved sophisticated regulation mechanisms to export virulence factors across the bacterial cell envelope to sense and respond to environmental changes. In this study, the genomic evolution and virulence-associated genes of CH06 are analyzed, providing a basis for research on the genomic evolution and pathogenic mechanisms of this fish pathogen in China.