In this study, vibrio parahaemolyticusisolate 229 isolated from frozen sea fish was carried out by genome sequencing, and gene annotation was performed by gene functional analysis to elucidate its pathogenic factors, which could provide clues and genome-scale data for investigating its pathogenic mechanism. We have accomplished the genome sequencing of V. parahaemolyticus 229 and assembled its genome using the obtained paired-end sequencing reads generated on the Illumina Hiseq 2000 Genome Analyzer. The assembled genome was 4.97 Mb in size with GC content of 43.90%. 4,940 protein coding sequences (CDSs) were predicted by gene prediction, of which 1,304 CDSs were annotated with GO function. WEGO illustration revealed that a series of CDSs might play important roles in theinvasion of the host of V. parahaemolyticus and subsequent metabolic processes. And an array of pathogenic virulence factor genes were annotated including hemolysin and Type III secretion system, which were gathered in different contigs and might act as independent pathogenic factors. The assembled genome and functional annotation of V. parahaemolyticus 229 could provide valuable information for further investigating the genetic basis of its pathogenicity.