A novel actinomycete, designated KLBMP 1221(T), was isolated from the surface-sterilized seeds of an oil-seed plant Jatropha curcas L. collected from Sichuan Province, south-west China and was characterized taxonomically by using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequence showed that this strain formed a distinct phyletic line within the radiation of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain KLBMP 1221(T) was most closely related to Amycolatopsis eurytherma NT202(T) (98.9%), Amycolatopsis tucumanensis ABO(T) (98.8%), Amycolatopsis thermoflava N1165(T) (98.6%) and Amycolatopsis methanolica IMSNU 20055(T) (98.5%). Strain KLBMP 1221(T) had morphological and chemotaxonomic properties that were consistent with its classification in the genus Amycolatopsis. However, DNA-DNA relatedness data and phenotypic differences clearly distinguished the isolate from its closest relatives. Based on the combined genotypic and phenotypic evidence, it is proposed that strain KLBMP 1221(T) be classified as representative of a novel species for which the name Amycolatopsis endophytica sp. nov. is proposed. The type strain is KLBMP 1221(T) (= KCTC 19776(T) = CCTCC AA 2010003(T)).