A bacterial strain, designated TMd3a3T, was isolated from a freshwater sample collected from the Tamagawa River in Japan. The cells of strain TMd3a3T were facultatively anaerobic, Gram-stain-negative, non-spore-forming rods that showed gliding motility. This strain was capable of denitrification and anaerobic growth with nitrate. Cloned 16S rRNA gene sequences of strain TMd3a3T yielded three different sequences (similarity between the three sequences: 98.9-99.7 %). The 16S rRNA gene sequences of strain TMd3a3T showed high similarity to those of Flavobacterium tructae 435-08T (97.2-97.4 % similarity), F. resistens BD-b365T (96.7-97.4 %), F. maotaiense T9T (97.0-97.3 %), F. limicola ST-82T (96.5-97.3 %), F. aquidurense WB 1.1-56T (96.9-97.2 %), F. spartansii T16T (96.9-97.2 %) and F. psychrolimnae LMG 22018T (96.4-97.0 %). Strain TMd3a3T contained menaquinone 6 as the sole respiratory quinone. The major cellular fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1�s7c and/or C16 : 1�s6c). The polar lipids were phosphatidylethanolamine, five unidentified aminolipids and five unidentified polar lipids. The DNA G+C content was 36.5 mol %. The DNA-DNA relatedness values of strain TMd3a3Twith F. tructae CCUG 60100T, F. resistens DSM 19382T, F. maotaiense JCM 19927T, F. limicola DSM 15094T, F. aquidurense DSM 18293T, F. spartansii ATCC BAA-2541T and F. psychrolimnae DSM 16141T were below 13 %. From the chemotaxonomic and physiological data and the levels of DNA-DNA relatedness, strain TMd3a3T should be classified as the representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium aquicola sp. nov. (type strain TMd3a3T=JCM 30987T=DSM 100880T) is proposed.