A 16-year-old female with cystic fibrosis (CF) presented with an acute respiratory exacerbation during which black flecks were observed in the spontaneously expectorated sputum. The production of this pigmented sputum was subsequently attributed to Exophiala dermatitidis hyphae. Treatment with antibiotics, corticosteroids, and antifungal medications led to an initial resolution of symptoms and clearance of the black pigment from her sputum. However, the patient again presented nine months later with reappearance of the pigmented flecks and concomitant clinical deterioration and was subsequently treated with an extended course of voriconazole. To the authors' knowledge, this is the first case report of fungal colonization by E. dermatitidis presenting as black flecks spontaneously expectorated in CF sputum.