Phaeohyphomycosis is a collection of superficial cutaneous, subcutaneous and(or) systemic infections caused by diverse dematiaceous fungi. The clinical records and clinical samples collected from a patient with a diagnosis of skin and subcutaneous phaeohyphomycosis progressed to disseminated phaeohyphomycosis were subjected to assays for potential genetic and immune defects that might associate with the infection. Two new compound heterozygous missense mutations on caspase recruitment domain-containing protein 9 gene (CARD9) (p.R35Q and p．E81K) were detected. Compared with the healthy donors, the proportions of Th1 and Th17 cells in the patient’s peripheral blood lymphocytes (PBLs) were low and the patient’s peripheral blood mononuclear cells (PBMCs) had impaired innate and adaptive immune responses against Phialophora verrucosa (P. verrucosa). The results indicated that CARD9 protein may play an important role in the pathogenesis of phaeohyphomycosis.