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Microsporum canis is a common zoophilic dermatophyte, which causes a range of infections. To explore the pathogenic mechanism of tinea capitis, we used the suppression subtractive hybridization (SSH) technique to investigate the differences in gene expression between different cultures of Microsporum canis incubated on three different types of mineral media containing child glabrous skin, child scalp tissue and adult scalp tissue. Using dot-blot hybridization and real-time PCR technique, we successfully screened and identified a pair of genes that had expression levels 44.6 and 117 times higher in culture 1 (M. canis cultured in mineral medium with child scalp tissue) than in culture 2 (M. canis cultured in mineral medium with glabrous skin tissue), and another pair of genes with expression levels 78.2 and 9.8 times higher in culture 1 than in culture 3 (M. canis cultured in mineral medium with adult scalp tissue). These four genes were found to have 41%, 53%, 40% and 94% homology to those encoding a hypothetical protein [family of serine hydrolases 1; (FSH1)], PQ loop repeat protein (PQ-LRP), a predicted protein [porphyrin galactose 4; (P-GAL4)] and NADH dehydrogenase subunit (NADH)1, respectively. The upregulation of the FSH1, PQ-LRP, P-GAL4 and NADH1 genes in cultures of child scalp tissue indicates that they are essential in the pathogenesis of tinea capitis caused by M. canis.