Shewanella algae is an aquaculture pathogen and an emerging human pathogen. There are increasing reports of carbapenem resistance S. algae from different hosts. However, little is known about the carbapenem-resistant S. algae in aquaculture and the genetic basis of these resistant bacteria in the special niche remains largely unknown. With the progress of sequencing technologies, it became possible to detect the multiple molecular mechanisms leading to antimicrobial resistance using whole genome sequencing data. In this study, we conduct a genome-scale investigation of S. algae SYT4, a carbapenem-resistant bacterium from cultured Asian hard clam in Taiwan. Whole-genome sequencing of Shewanella algae SYT4 was performed using Illumina MiSeq platform. The genome size of Shewanella algae SYT4 is 4,838,024 bp in length. The DNA G + C content is 53.09%. It encodes 4207 proteins and 104 RNA genes. The phylogenetic relationships of S. algae SYT4 and related Shewanella strains were determined using average nucleotide identity and 16S rRNA gene sequence. Candidate genes for antimicrobial resistance and virulence were identified. S. algae SYT4 carries bla(OXA-55) and multiple genes encoding efflux pumps. In addition, genes related to chemotaxis, biofilm formation, and stress response were identified, suggesting potential pathogenic mechanism. We demonstrate that whole-genome sequencing is capable to decipher the resistance determinants of carbapenem-resistant bacterium associated with aquaculture. The panoply of antibiotics resistance genes found suggests the organisms can act as a reservoir of antimicrobial drug resistance determinants in seafood, which is an issue of considerable concern.