The Gram-stain-negative, rod-shaped, aerobic strain, designated YC1039(T), was isolated from a seamount northern Mariana Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YC1039(T) was related to the genus Mesoflavibacter and had highest 16S rRNA gene sequence similarities to Mesoflavibacter sabulilitoris GJMS-9(T) (98.3%) and Mesoflavibacter zeaxanthinifaciens TD-ZX30(T) (98.2%). The predominant cellular fatty acids were iso-C-15:1 G and iso-C-15:0. The polar lipid profile contained phosphatidylethanolamine, two unidentified phospholipids, and 13 unidentified lipids. The respiratory quinone was MK-6. The genomic DNA G+C content of strain YC1039(T) was 29.8 mol%. On the basis of the evidence presented in this study, strain YC1039(T) represents a novel species of the genus Mesoflavibacter, for which we propose the name Mesoflavibacter profundi sp. nov. (type strain YC1039(T)= KACC 19026(T)=CGMCC 1.16329(T)).