We report a rare case of onychomycosis due to Arthrographis kalrae, and describe an attempt to elucidate the source of the infection by fungal isolation and PCR-based methods for detection of A. kalrae. The patient was a 63-year-old Japanese man, whose fingernails, excluding the right index finger, were markedly dystrophic. Microscopic examination of his fingernails disclosed hyaline hyphae and arthroconidia. The causal agent was identified as A. kalrae based on morphological characteristics and ITS region sequencing. The fungus was susceptible in vitro to terbinafine, itraconazole, and miconazole. A therapeutic trial of oral terbinafine, 125 mg/day and topical 1% miconazole for seven months brought about a complete cure of the ungual lesion. We found that A. kalrae could be detected at 1.1 x 10(4) CFU/g (92.4% incidence) in soil from the patient's garden. Furthermore, varying CFUs of A. kalrae were recovered in 61% of the samples obtained from crop field soils, commercially available soils or allied products for gardening. Since the patient was working with soil that harbored A. kalrae, the possibility of acquiring the infection from this source should not be excluded.