A novel Gram-staining-negative, aerobic, non-motile, yellow-to-orange carotenoid-type-pigmented and rod-shaped bacterium, designated strain WP25T, was isolated from the intestine of a comb pen shell, Atrina pectinata, which was collected from the South Sea near Yeosu in Korea. The isolate grew optimally at 20 °C, at pH 7 and with 2% (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain WP25T belonged to the genus Polaribacter in the family Flavobacteriaceae and the highest sequence similarity was shared with the type strain of Polaribacter sejongensis (98.5%). The major cellular fatty acids were iso-C15:0, anteiso-C15:0, C15:1ω6c and iso-C15:0 3-OH. The main respiratory quinone was menaquinone MK-6. The polar lipids of strain WP25T were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content was 31.2 mol%. DNA-DNA hybridization experiments indicated <12.6% genomic relatedness with closely related strains. Based on phylogenetic, phenotypic and genotypic analyses, strain WP25T represents a novel species in the genus Polaribacter, for which the name Polaribacter atrinae sp. nov. is proposed, with the type strain WP25T (=KACC 17473T=JCM 19202T).