Abstract: Objective To report a case of Majocchi′s granuloma induced by var. raubitschekii of Trichophyton rubrum, and to evaluate the relationship between deep and superficial fungal infection with genotyping technique. Methods The patient underwent physical, pathological and mycologic examination, which included microscopic observation, fungal culture, and urease reaction. The sequence of intertranscribed spacer （ITS） of rDNA was analysed by PCR and sequencing. Isolates from affected toes and tissue as well as one reference strain and six clinical strains of T. rubrum. were subjected to analysis of the tandem repeat subelement（TRS-1） in nontranscribed spacer（NTS）of rDNA by PCR. Results A 48-year-old female patient presented with a 2-month history of red papules and nodular lesions on the back, buttock and thigh, as well as a 3-year history of onychomycosis which had become more severe after a liver transplantation 9 months before. Pathological and mycologic examinations confirmed the diagnosis of Majocchi′s granuloma. The pathogen was identified as var. raubitschekii of T. rubrum by microscopic examination, fungal culture, positive urease reaction and the sequence of ITS. As shown by the amplications of TRS-1 of NTS, the genotypes of strains from affected nails and tissue were identical, but differed from those of other clinical strains of T. rubrum. Conclusions There is a polymorphism in TRS-1 of rDNA NTS of T. rubrum, with the genotypes of isolates from affected nails and tissue being identical, which suggests they are of the same origin.