Candida glabrata was continuously isolated in cultured urine samples from a subject with thrombotic thrombocytopenic purpura. Yeast-like fungal phagocytosis found in gram staining led to agents being tested for antifungal susceptibility, revealing hyposensitivity to micafungin (MCFG) of MIC <2 mg/mL. MCFG administered for 10 days failed to cure C. glabrata infection. To clarify why hyposensitivity occurred, we analyzed the FKS gene sequence using the PCR, finding a deficit of 3 bases coding phenylalanine at FKS2 gene amino acid 659. MCFG hyposensitivity may thus occur in long-term candin-class anti-fungal agent treatment. Candin-class agents have potent anti-fungal activity with fewer adverse effects and are widely used clinically. Hyposensitivity due to resistant C. glabrata species showed thus be considered in fungal infection treatment.