In this article, we research the phylogenetic position of the rare endemic banana, Musa huangbaioa, which was described only in Chinese journal in 1987. This banana was found at the foot of the Mount Emei in Sichuan Province and has remarkable morphological features, e. g., undulated petiole margins, ribbed fruits and irregular form of the seeds, which are rather unusual in the genus and distinguish it from all other species. In addition, due to its uncertain affinity, we researched the position of M. huangbaioa in the Musaceae family with the aid of molecular phylogenetic analysis of two marker sequences, nrITS and trnL-trnF. We found that this species belongs to the large and rather complicated group of Chinese bananas, M. basjoo-M. itinerans clade. According to the ITS data, M. huangbaioa is monophyletic with one M. basjoo specimen that was cultivated in Central America. Probably, this fact represents that this species can be modern hybrid with one of the genomes inherited from M. basjoo s. l. The whole group M. basjoo-M. itinerans, which M. huangbaioa belongs to, is well separated within the sect. Musa and could be prone to frequent hybridizations in the natural environment; it requires an additional research for more precise differentiation of the group.