Two novel bacterial strains, designated SYP-B540T and SYP-B556, were isolated from rhizospheric soil of Panax notoginseng located at Yunnan Province, China. Both strains were Gram-staining negative, aerobic, non-motile, elongated rod shaped and yellow coloured. They grew optimally at 28 °C and pH 7.0. Analysis of 16S rRNA gene sequences showed that the two strains shared 99.8 % sequence similarity to each other, but lower than 97.6 % to the other known species of the genus Flavobacterium. The predominant respiratory quinone for the two strains was MK-6, and the major fatty acids were iso-C15:0 and summed Feature 3 (comprising 16:1 ω7c and/or 16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine, two unidentified polar lipids and three unidentified amino-phospholipids. The DNA G+C contents of strains SYP-B540T and SYP-B556 were 33.3 and 32.7 mol%, respectively. In addition, the DNA–DNA hybridization values of strains SYP-B540T and SYP-B556 to their closest phylogenetic neighbors were significantly lower than 70 %. On the basis of the polyphasic taxonomy studies, strains SYP-B540T and SYP-B556 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium notoginsengisoli sp. nov. is proposed. The type strain is SYP-B540T (=KCTC 32505T = NBRC 110012T = BCRC 80724T).