Dominant bacteria (SX1) were isolated from diseased and dead megalopas Portunus trituberculatus, and have pathogenicity to healthy megalopa and juvenile (Ⅲ) crab Portunus trituberculatus by artificial challenge. The phenotypic characteristics of the isolates including morphological, physiological and biochemical characteristics were determined. The 16S rRNA and two housekeeping genes, RNA polymerase a-chain (rpoA) and DNA gyrase B subunit (gyrB) were sequenced, and the phylogenetic trees based on 16S rRNA and gyrB sequences were constructed as an aid to identification. The sequenced 16S rRNA gene of strain SX1 (GenBank accession No. JQ394838) was 1454bp, the gyrB gene of strain SX1 (GenBank accession No. JQ394839) was 1077bp, the rpoA gene (GenBank accession No. JQ394840) was 913bp. The 16S rRNA, gyrB and rpoA genes were compared with sequences deposited in databases, molecular phylogenetic analyses were conducted. The results showed that the characteristics of identified strain (SX1) consist with genus of Photobacterium, and the 16S rRNA, gyrB and rpoA genes of the identified strain (SX1) exhibited high similarity with Photobacterium sp., the phylogenetic trees constructed using the neighbor joining method based on 16S rRNA and gyrB genes, strain SX1 clustered with the Photobacterium ganghwense, and was supported by a higher bootstrap value. Therefore, strain SX1 was similar with P.ganghwense. The results confirmed that the diseased megalopas were infected by P.ganghwense. To our knowledge, this is the first report of P.ganghwense as pathogenic bacteria of crab.The study showed the diversity and complexity of pathogenic bacteria from aquatic animals.