A novel bacterium (strain YIM 65583(T)) belonging to the genus Sphingomonas was isolated from surface-sterilized tissue of Artemisia annua L., which was collected from Yunnan province, south-west China. Its morphology, physiology and biochemical features were consistent with those of members of the genus Sphingomonas. Analysis of the 16S rRNA gene sequence of strain YIM 65583(T) further confirmed that it should be classified as a member of the genus Sphingomonas and was most closely related to Sphingomonas phyllosphaerae FA2(T) (99.7%) and Sphingomonas yunnanensis YIM 003(T) (98.3%). The isolate was Gram-negative and formed yellow-pigmented colonies on ISP 2 medium. It grew optimally at pH 6.0-8.0, at 20-37 °C and in the presence of 0-1% (w/v) NaCl. The major respiratory lipoquinone was ubiquinone-10; C(18:1)ω7c, anteiso-C(16:1), C(14:0)-2OH, C(17:1)ω6c, C(16:0) and C(15:0) were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. The G+C content of the genomic DNA was 63.3 mol%. The DNA-DNA relatedness values of the isolate YIM 65583(T) with S. phyllosphaerae FA2(T) and S. yunnanensis YIM 003(T) were 43.1% and 37.9%, respectively. Based on these features, it is concluded that the strain represents a novel species of the genus Sphingomonas, for which the name Sphingomonas endophytica sp. nov. is proposed, with YIM 65583(T) (=CCTCC AA 209035(T)=JCM 17394(T)) as the type strain.