A novel actinobacterial strain, designated S2509, was isolated from marine sediment collected by a dredge at a depth of 45 m along Melet River offshore of the southern Black Sea coast, Ordu, Turkey. The cell wall peptidoglycan of strain was found to contain meso-diaminopimelic acid and 3-OH-diaminopimelic acid. The whole cell sugars detected were arabinose, glucose, rhamnose, ribose and xylose. The diagnostic phospholipids of strain S2509 were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, a glycolipid and two unidentified phospholipids. The predominant menaquinones were identified as MK-9(H), MK-9(H), MK-10(H), MK-9(H), MK-10(H) and MK-10(H). The major cellular fatty acids were found to be iso-C, iso-C and 10-methyl C. The taxonomic position of the strain was established using a polyphasic approach, showing that S2509 strain belongs to the genus Micromonospora. Phylogenetic analysis based on the 16S rRNA gene sequence of strain S2509 showed that it is closely related to the type strain of Micromonospora chokoriensis DSM 45160 (99.37% sequence similarity), and phylogenetically clustered with Micromonospora inaquosa LB39 (99.37%), Micromonospora lupini Lupac 14N (99.16%), Micromonospora violae NEAU-zh8 (99.23%) and Micromonospora taraxaci NEAU-P5 (99.03%). The phylogenetic analysis based on the gyrB gene sequence of strain S2509 confirmed its close relationship with M. chokoriensis JCM 13247 (96.5% sequence similarity). Whole genome sequences confirmed by digital DNA-DNA hybridization analysis that the strain S2509 represents a novel species in the genus Micromonospora, for which the name Micromonospora orduensis sp. nov. is proposed. The type strain is S2509 (=DSM 45926 = KCTC 29201).