Isolation of novel actinobacteria from unexplored habitats as potential sources of novel drug leads has utmost importance. During the course of screening arid soil samples for novel actinobacteria, strain H3C3^T was isolated from Malatya, Turkey and its taxonomic position was revealed by a genome-based polyphasic approach. Pairwise sequence comparison of the 16S rRNA gene showed that the strain is closely related to Actinomadura fibrosa JCM 9371^T with sequence identity level of 99.0%. Comparative genome analyses based on digital DNA-DNA hybridization and average nucleotide identity indicated that strain H3C3^T represents a novel species within the genus Actinomadura. The strain has typical characteristics of the genus Actinomadura, i.e. meso-diaminopimelic acid as diagnostic amino acid; galactose, glucose, madurose and ribose as whole-cell sugars. Major menaquinones detected were MK-9(H₆), MK-9(H₈) and polar lipids were diphosphatidylglycerol, phosphatidylinositol, glycophospholipid and unknown phospholipid and lipids. Its genome size is approximately 10.2 Mb with G+C content of 71.6%. Further genomic analyses of strain H3C3^T indicated its high potential for novel biosynthetic gene clusters coding for various chemical structures. On the basis of phenotypic and phylogenetic analyses, strain H3C3^T represents a novel species of the genus Actinomadura, for which Actinomadura rubrisoli sp. nov. is proposed, and it holds high promise for novel biosynthetic metabolites of value to biopharmaceutical industry.