Terbinafine (TBF)-resistant anthropophilic dermatophytes have recently been isolated from human patients around the world. Almost all TBF-resistant strains of dermatophytes have the amino acid substitution in the squalene epoxidase (SQLE) gene. In this study, we performed whole genome sequencing of a TBF-resistant Microsporum canis strain (designated 47C) to clarify the mechanisms underlying TBF- resistance conferred by genetic mutations. Strain 47C, isolated from a cat with feline dermatophytosis in China in 2018, was previously identified as the first TBF-resistant M. canis. Approximately 2.5 µg of genomic DNA sample was extracted from growing mycelium of 47C and sequenced using a PacBio Sequel IIe system. We mapped the 23.2 Mb genome against the reference M. canis CBS 113480 strain (assembly ASM15114v1 in GenBank) and identified 1,455 genetic variations, including substitutions, insertions and deletions (INDELs). Our analysis initially focused on whether mutations existed in the SQLE gene, which is known to encode SQLE. We discovered a T→C mutation at 1183 bp (F395L mutation) in the putative SQLE gene of strain 47C. In contrast, seven TBF-susceptible strains exhibited no mutations in their SQLE genes. The F395L mutation likely reduces the affinity of TBF for SQLE in M. canis, similar to the F397L mutation found in TBF-resistant Trichophyton rubrum and Trichophyton interdigitale.