A Gram-stain-positive, aerobic, coccoid, non-motile, non-spore-forming bacterium, designated strain S3Af-1T, was isolated from surface-sterilized bark of Bruguiera sexangula collected from Dongzhaigang National Nature Reserve in Hainan, China, and examined using a polyphasic approach to clarify its taxonomic position. This bacterium did not produce substrate mycelia or aerial hyphae, and no diffusible pigments were observed on the media tested. Strain S3Af-1T grew optimally without NaCl, at 28-30 °C and at pH 7.0.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S3Af-1T belonged to the genus Microlunatus and shared highest similarity with 'Microlunatus terrae' BS6 (97.43 %) and Microlunatus soli CC-12602T (97.08 %). DNA-DNA hybridization results indicated that the level of relatedness between strain S3Af-1T and M. soli CC-12602T was less than 70 %. The DNA G+C content of strain S3Af-1T was 67.1 mol%. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid. MK-9(H6) and MK-9(H4) were the predominant menaquinones. Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, two unidentified phospholipids and other lipids were detected in the polar lipid extracts. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. On the basis of phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, strain S3Af-1T represents a novel species of the genus Microlunatus, for which the name Microlunatus endophyticus sp. nov. is proposed. The type strain is S3Af-1T ( = DSM 100019T = CGMCC 4.7306T).