A Gram-staining-negative, motile, non-spore-forming and rod-shaped bacterial strain, $20-23R^T$, was isolated from intestine of bensasi goatfish, Upeneus bensasi, and its taxonomic position was investigated by using a polyphasic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain $20-23R^T$ belonged to the genus Shewanella. Strain $20-23R^T$ exhibited 16S rRNA gene sequence similarity values of 99.5, 99.2, and 97.5% to Shewanella algae ATCC $51192^T$, Shewanella haliotis $DW01^T$, and Shewanella chilikensis $JC5^T$, respectively. Strain $20-23R^T$ exhibited 93.1-96.0% 16S rRNA gene sequence similarity to the other Shewanella species. It also exhibited 98.3-98.4% gyrB sequence similarity to the type strains of S. algae and S. haliotis. Strain $20-23R^T$ contained simultaneously both menaquinones and ubiquinones; the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-8 and Q-7. The fatty acid profiles of strain $20-23R^T$, S. algae KCTC $22552^T$ and S. haliotis KCTC $12896^T$ were similar; major components were iso-$C_{15:0}$, $C_{16:0}$, $C_{16:1}$ ${omega}7c$ and/or iso-$C_{15:0}$ 2-OH and $C_{17:1}$ ${omega}8c$. The DNA G+C content of strain $20-23R^T$ was 53.9 mol%. Differential phenotypic properties and genetic distinctiveness of strain $20-23R^T$, together with the phylogenetic distinctiveness, revealed that this strain is distinguishable from recognized Shewanella species. On the basis of the data presented, strain $20-23R^T$ represents a novel species of the genus Shewanella, for which the name Shewanella upenei sp. nov. is proposed. The type strain is $20-23R^T$ (=KCTC $22806^T$ =CCUG $58400^T$).