A Gram-negative, motile, rod-shaped, non-spore-forming bacterial strain, designated as Ko03$^T$, was isolated from microbial granules, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The isolate was positive for catalase and oxidase, but negative for gelatinase and $eta$-galactosidase. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbors being Comamonas koreensis KCTC 12005$^T$ (95.9% sequence similarity), Comamonas nitrativorans DSM 13191$^T$ (95.7%), and Comamonas odontotermitis LMG 23579$^T$ (95.7%). Strain Ko03$^T$ had a genomic DNA G+C content of 68.4 mol % and the predominant respiratory quinone was Q-8. The major fatty acids were C$_{16:1}$ $omega$7c (44.7%), C$_{16:0}$ (28.1 %), C$_{18:1}$ (16.1 %), and C$_{10:0}$ 3-OH (3.5%). These chemotaxonomic results supported the affiliation of strain Ko03$^T$ to the genus Comamonas. However, low 16S rRNA gene sequence similarity values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Ko03$^T$ from recognized Comamonas species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Ko03$^T$ represents a novel species of the genus Comamonas, for which the name Comamonas granuli sp. nov. is proposed. The type strain is Ko03$^T$(= KCTC 12199$^T$= NBRC 101663$^T$).