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A Gram-positive-staining, facultatively aerobic, endospore-forming bacterial strain, isolated from the stem tissue of cotton (Gossypium hirsutum) was subjected to a detailed taxonomic study using a polyphasic approach. Based on 16S rRNA gene sequence similarity comparisons, strain JM-1350(T) grouped into the genus Saccharibacillus, and was most closely related to the type strain of Saccharibacillus sacchari (96.5% 16S rRNA gene sequence similarity), followed by the type strains of Saccharibacillus kuerlensis (96.3%) and Saccharibacillus deserti (95.1 o/o). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system contained exclusively menaquinone MK-7. The polar lipid (L1) profile consisted of the major lipids diphosphatidylglycerol and phosphatidylglycerol and moderate amounts of three glycolipids and an aminophospholipid and a polar lipid (L1). The major fatty acids were iso- and anteiso-branched fatty acids. The genomic G+C content was 55.2 mol%. In addition, the results of physiological and biochemical tests allowed phenotypic differentiation of strain JM-1350(T) from all closely related species. Thus, strain JM-1350(T) represents a novel species of the genus Saccharibacillus, for which the name Saccharibacillus endophyticus sp. nov. is proposed. The type strain is JM-1350(T) (=LMG 29710(T)=CCM 8702(T)).