Background  An 81-year-old man presented with a skin ulcer on the left forearm caused by infection with Mycobacterium ulcerans ssp. shinshuense. The patient first noticed the subcutaneous nodule with an undermined ulcer and areola on the left forearm without any episode of trauma.

Methods  The rod-shaped and acid-fast bacteria taken from the ulcerative lesion were positive for Ziehl–Neelsen staining. The bacterial colony was cultured on Ogawa slant egg medium at 28 °C.

Results  A clinical diagnosis of Mycobacterium infection was made. For therapy, in addition to oral clarithromycin, topical sulfadiazine silver and hyperthermia were used. One month after starting treatment, topical treatment was changed to U-pasta (sucrose, povidone-iodine). Four months after the onset of the disease, bacterial colonies composed of scotochromogens were identified as Mycobacterium marinum by the DNA–DNA hybridization (DDH) method. The growth speed and characteristics of the bacterial colonies were different from those of Mycobacterium marinum.

Conclusions  This pathogenetic bacterium was finally identified as Mycobacterium ulcerans ssp. shinshuense by the polymerase chain reaction method and 16S rRNA gene sequencing. Nine months after the onset of the disease, the ulcer was re-epithelialized with a residual scar.