A Gram-negative, strictly aerobic, chemoheterotrophic, pale-yellow pigmented, non-motile, rod-shaped bacterial strain, designated MN1-138(T), was isolated from water in the tidal zone at the estuary of Heita river, Iwate, Japan, using an in situ cultivation technique. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel isolate is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, and the highest sequence similarities were found with the species Wenyingzhuangia heitensis H-MN17(T) (97.3%). The DNA-DNA relatedness between values between strains MN1-138(T) and W. heitensis H-MN17(T) was 34%. The DNA G+C content of strain MN1-138(T) was determined to be 33.1 mol%; MK-6 was identified as the major menaquinone; and the presence of iso-C15:0, iso-C15:0 3-OH, and iso-C17:0 3-OH as the major (>10%) cellular fatty acids. A polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified glycolipids, and two unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species of the genus Wenyingzhuangia for which the name Wenyingzhuangia aestuarii sp. nov. is proposed. The type strain of W. aestuarii sp. nov. is MN1-138(T) (=KCTC 42780(T) = NBRC 111505(T)).