Recently, the characteristics of prevalent bacterial pathogens causing bovine mastitis have become increasingly complicated, and many commensal or unusual bacterial species have been isolated from milk samples of cows with mastitis. Strain JS20170427COW was isolated dominantly from the milk of Holstein Friesian cows with mastitis in Jiangsu province in China. Colonies of this strain showed a hillock-like protrusion, with a pale-yellow color at the protrusion and a transparent edge, 4–5 mm in diameter after cultivation at 37 °C for 24 h on 5% sheep blood-enriched agar. Although 16 s rRNA analysis showed the closest relationship with the family Flavobacteriaceae containing Elizabethkingia spp., Riemerella sp. and Soonwooa buanensis, the bacterial species of strain JS20170427COW could not be identified adequately because it had a sequence identity of less than 95 % in 16 s rRNA when compared with all the known species of the family Flavobacteriaceae. Unexpectedly, both the first and re-sequencing data determined the whole genome size of strain JS20170427COW to be 2.69 Mb, which is different from the above three closest bacterial species. Therefore, we hypothesized that strain JS20170427COW is a novel taxon of Flavobacteriaceae. Further identification using conserved genes, single-nucleotide polymorphisms (SNPs), phylogenetic and average nucleotide identity analyses based on whole genome data suggested that JS20170427COW was more likely to be an Elizabethkingia-like strain, but that it does not belong to the Elizabethkingia genus. Comparison of the predicted open reading frames (ORFs) revealed that strain JS20170427COW encodes more special genes than Elizabethkingia species. In summary, we identified a novel Flavobacteriaceae taxon showing a close relationship with Elizabethkingia subspecies, which has potential pathogenicity in bovine mastitis.