A novel endophytic actinomycete, strain YIM 65646(T), was isolated from the roots of Artemisia annua L. collected from Yunnan Province, south-west China. Growth was observed in the temperature range 10-40 °C (optimum 20-28 °C) and at pH 6.0-9.0 (optimum pH 7.0). The organism formed well-developed, branched substrate mycelia, but aerial mycelium was not produced. Phenotypic characterization and 16S rRNA gene sequence analysis indicated that strain YIM 65646(T) belonged to the family Micromonosporaceae (sharing ≤93.6% sequence similarity with members of this family) and formed a distinct clade in the Micromonosporaceae phylogenetic tree. The strain contained meso-diaminopimelic acid in the cell wall and mannose, ribose, galactose and glucose in whole-cell hydrolysates. The major menaquinones were MK-10(H(4)), MK-10(H(2)), MK-8(H(2)), MK-9(H(2)) and MK-10(H(6)). The major fatty acids were iso-C(15:0), anteiso-C(15:0), anteiso-C(17:0), iso-C(17:0) and iso-C(16:0). The DNA G+C content of strain YIM 65646(T) was 70.0 mol%. On the basis of morphological and chemotaxonomic properties and phylogenetic analysis based on 16S rRNA gene sequence data, it is proposed that this strain should be classified in a novel genus and species, Phytomonospora endophytica gen. nov., sp. nov., in the family Micromonosporaceae. The type strain is YIM 65646(T) (=CCTCC AA 209041(T) =DSM 45386(T)).