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A novel endophytic actinomycete strain GKU 173T isolated from the roots of Acacia mangium Willd. showed potential plant growth promoting (PGP) activity. Phylogenetic analysis, based on 16S rRNA gene, indicated that strain GKU 173T was the most closely related to Fodinicola feengrottensis HKI 0501T—the only species in the genus Fodinicola. Morphology and chemotaxonomy of strain GKU 173T indicated that it belongs to the genus Fodinicola by having meso-diaminopimelic acid in the cell wall and xylose as the characteristic cell-wall sugars. The cellular fatty acid profile mainly comprised iso-C16:0, anteiso-C17:0, iso-C18:0, and iso-C17:0. The major menaquinones were MK-9(H4), MK-9(H6), and MK-9(H8). The main polar phospholipids contained diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylinositol (PI). Genome analysis signified DNA G+C content of 67.81 mol%. The level of digital DNA-DNA relatedness between strain GKU 173T and the type strain was 21.30%. On the basis of polyphasic characteristics, strain GKU 173T clearly represents a novel species of the genus Fodinicola, for which the name Fodinicola acaciae sp. nov. (= TBRC 10620T = NBRC 114213T) is proposed. Furthermore, genome analysis of both strains suggested that members of the genus Fodinicola are promising sources of beneficial PGP-actinomycetes and novel secondary metabolites.