An endophytic fungal species of Exophiala was isolated from the fruits of Amomum tsao-ko during an investigation of the fungal diversity associated with A. tsao-ko in Honghe Prefecture, Yunnan Province, China. Morphological characteristics and the combined internal transcribed spacer (ITS), large subunit nuclear rDNA (LSU), and small subunit nuclear ribosomal rDNA (SSU) loci phylogenetic analysis confirmed the new isolate is a new species, Exophiala hongheensis. Phylogenetically, E. hongheensis is related to E. lavatrina, E. lecanii-corni, and E. mali; however, it can be distinguished from them by its smaller conidia and conidiogenous cells on the lateral side of the mycelium. Descriptions, illustrations, and phylogenetic analysis results of E. hongheensis are provided herein.