A novel Gram-negative, capnophilic, fusiform bacterium, designated strain ChDC OS43(T), was isolated from a human refractory periapical abscess in the left mandibular second molar and was characterized by polyphasic taxonomic analysis. The 16S rRNA gene sequence revealed that the strain belongs to the genus Capnocytophaga, as it showed sequence similarities to Capnocytophaga ochracea ATCC 27872(T) (96.30%) and C. sputigena ATCC 33612(T) (96.16%). The prevalent fatty acids of strain ChDC OS43(T) were isoC(15:0) (57.54%), C-16:0 (5.93%), C-16:0 3OH (5.72%), and C-18:1 cis 9 (4.41%). The complete genome of strain ChDC OS43(T) was 3,412,686 bp, and the G+C content was 38.2 mol%. The average nucleotide identity (ANI) value between strain ChDC OS43(T) and C. ochracea ATCC 27872(T) or C. sputigena ATCC 33612(T) was > 92.01%. The genome-to-genome distance (GGD) value between strain ChDC OS43(T) and C. ochracea ATCC 27872(T) or C. sputigena ATCC 33612(T) was 32.0 and 45.7%, respectively. Based on the results of phenotypic, chemotaxonomic, and phylogenetic analysis, strain ChDC OS43(T) (= KCOM 1579(T) = KCTC 5562(T) = KCCM 42841(T) = JCM 32133(T)) should be classified as the type strain of a novel species of genus Capnocytophaga, for which the name Capnocytophaga endodontalis sp. nov. is proposed.