Canine and feline upper respiratory tract (URT) infection due to Aspergillus spp. is considered an emerging disease, with the number of reported cases continuing to rise in Japan. Aspergillus fumigatus has been the most frequently reported etiologic agent of sino-orbital aspergillosis in dogs and cats; the other Aspergillus species, Aspergillus felis, Aspergillus fischeri, Aspergillus udagawae, Aspergillus viridinutans, and A. fumigatus, have also been implicated in feline cases. The minimum inhibitory concentrations (MICs) of antifungal drugs are elevated for these cryptic species compared with A. fumigatus. Some reports showed that the feline infections due to cryptic species did not respond to treatment with antifungal drugs. These results suggest that species identification and antifungal susceptibility testing of infecting agents are important to ensure effective treatment of feline URT aspergillosis. Feline cryptococcosis in Japan is typically attributed to Cryptococcus neoformans var. grubii. We isolated a fluconazole-resistant strain of C. grubii from a feline cryptococcosis. The predicted amino acid sequence of the lanosterol 14-α demethylase gene (ERG11) protein in the isolate was identical to that of the C. grubii reference strain. RT-PCR analysis of ERG11 and ATP binding cassette (ABC) transporter-encoding gene (AFR1) indicated that the isolate had increased transcription factor function for ERG11 and AFR1 compared with fluconazole-susceptible strains. This observation, in combination with the lack of resistance to other azoles (that is, lack of cross resistance), suggests that resistance in our isolate was the result of overexpression of the endogenous ERG11 and ABC transporter. Further ecological and epidemiological studies on small animal mycoses in Japan are needed to monitor the emergence of antifungal drug resistant strains.