Lophophyton gallinae (Microsporum gallinae) is a zoophilic fungus that causes ringworm in chickens and related species, and occasionally in humans. There are 45 human cases worldwide including a Japanese case from Okinawa in 2009. After the finding of the human L. gallinae case, 793 chickens in Japan, including 293 from the mainland and 500 from the Nansei Island areas, were investigated to determine the prevalence of dermatophytes and their related fungal species. The survey was carried out from December 2008 to March 2013. Various dermatophytes and related fungal species were isolated from the studied chickens, with a prevalence of 24.6%. In total, 224 dermatophytes and related species were isolated in the survey. The most commonly isolated species included, in descending order of frequency, Arthroderma multifidum, Aphanoascus terreus, and Chrysosporium spp. Ar. multifidum and Ap. terreus have no record of pathogenicity, and the present isolates of Chrysosporium spp. were not matched to pathogenic Chrysosporium spp. based on the ITS rDNA sequences. Interestingly, an L. gallinae isolate was detected in a male 10-month-old shamo (fighting cock) from the main island. Furthermore, one strain of Arthroderma simii was also isolated as the second record in Japan following that from an imported chimpanzee. Although L. gallinae and Ar. simii are likely to be endemic in our country, the transmission of dermatophytosis from chickens to humans is unlikely to occur because of the reduced chances for citizens to come in contact with chickens due to various factors.