A bacterial strain, designated CMJ-5(T), was isolated from a freshwater shrimp culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain CMJ-5(T) were Gram-stain-negative, strictly aerobic, non-motile, yellow-pigmented rods surrounded by a thick capsule. Growth occurred at 20-35 °C (optimum, 30 °C), at pH 6.5-8.0 (optimum, pH 7.0) and with 0-0.5% NaCl (optimum, 0%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CMJ-5(T) belonged to the genus Flavobacterium and was related most closely to Flavobacterium haoranii LQY-7(T) with sequence similarity of 94.4%. Strain CMJ-5(T) contained iso-C15:0 (37.5%), iso-C17:0 3-OH (13.4%), iso-C15:0 3-OH (13.1%) and iso-C15:1 G (11.2%) as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized aminophospholipids and phospholipids. The major polyamine was homospermidine. The G+C content of the genomic DNA was 42.4 mol%. On the basis of phylogenetic inference and phenotypic data, strain CMJ-5(T) should be classified as a representative of a novel species, for which the name Flavobacterium squillarum sp. nov. is proposed. The type strain is CMJ-5(T) (=BCRC 80405(T)=LMG 26890(T)=KCTC 23915(T)). Emended descriptions of Flavobacterium haoranii, Flavobacterium cauense, Flavobacterium terrae and Flavobacterium aquatile are also proposed.