Common scab (CS) disease of potato caused by soil- and seed-borne pathogenic Streptomyces, occurs throughout the potato-growing areas in Japan and elsewhere in the world. In Japan, at least three pathogenic Streptomyces species have been described to cause CS S. scabiei, S. turgidiscabies and S. acidiscabies. While genome sequences are available for many saprophitic Streptomyces, relative few genome sequences are available for pathogenic species. Here, we present draft genome sequences for pathogenic Streptomyces isolated in Kagoshima prefecture in Japan.