The zoophilic dermatophyte Trichophyton benhamiae has received attention due to increasing infections in human in recent years. Trichophyton benhamiae has been found on asymptomatic rodents from pet shops in several countries posing a potential risk for transmission to humans. The aim of this study was to determine the prevalence of positive dermatophyte cultures from rodents in Danish pet shops in order to clarify the magnitude of potential sources of zoophilic infections and to prevent further spread. Specimen sampling was performed in 17 Danish pet shops using the brush technique (MacKenzie technique). After incubation, cultures were sent to ITS DNA sequencing for molecular species identification. Pet shop employees were asked to fulfil a five-question survey regarding purchase and procedures of diseased animals. A total of 98 animals were sampled (N = 32 rabbits, N = 32 guinea pigs and N = 34 hamsters). Trichophyton benhamiae was found in 14/98 samples (14%); 12/32 guinea pigs (38%) were positive with T benhamiae, 2/34 (6%) hamsters and 0/32 rabbits (0%). We found that hamsters and particularly guinea pigs from Danish pet shops are common asymptomatic carriers of the dermatophyte T benhamiae. Although a larger study is warranted to test this postulate, and it raises the question if infection control measures should be implemented in pet shops.