Since the early 20th century, the taxonomic identity of Musa nagensium Prain (Musaceae) has been uncertain to most botanists. The aim of this paper is to clarify the taxonomic history of M. nagensium. A new variety, M. nagensium var. hongii Häkkinen, is described and illustrated here. This rare variety of M. nagensium was found only in a small area in northwestern Yunnan, China, near the Burmese border. This study is based on observed morphological characteristics in the field and from specimens in various herbaria, and is supported by the existing literature on the Musaceae. A key to M. nagensium and related taxa is provided.