A Gram-stain-positive, aerobic, non-motile, non-spore-forming and short-rod-shaped actinobacterium, designated strain 1T4Z-3, was isolated from a piece of surface-sterilized branch of Aegiceras corniculatum collected from the Cotai Ecological Zones in Macao, China. Comparative 16S rRNA gene sequence analysis showed that strain 1T4Z-3 was clearly affiliated to the genus Amnibacterium and exhibited 97.9% gene sequence similarity to Amnibacterium kyonggiense JCM 16463, 97.3% gene sequence similarity to Amnibacterium soli JCM 19015 and less than 96.4% gene sequence similarities to other genera of the family Microbacteriaceae. Strain 1T4Z-3 had L-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid. The major fatty acids (>10% of total fatty acids) were iso-C (46.6 %) and anteiso-C (27.3 %). The predominant menaquinones of strain 1T4Z-3 were MK-11 (81.4 %) and MK-12 (14.1 %). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids, four unidentified phospholipids and two unidentified lipids. The DNA G+C content of strain 1T4Z-3 was 71.4 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain 1T4Z-3 is considered to represent a novel species of the genus Amnibacterium, for which the name Amnibacterium endophyticum sp. nov. is proposed. The type strain of Amnibacterium endophyticum is 1T4Z-3T (=KCTC 39983=CGMCC 1.16066).