In this article, we compare the phylogenetic position of various specimens of the Japanese banana (Musa basjoo) originating from the greenhouses of the St. Petersburg Botanical Garden of Peter the Great and from the Kyoto Garden using the analysis of marker sequences ITS1-5.8S rRNA-ITS2 and trnL-trnF. Samples of M. basjoo grown in the Peter the Great Botanical Garden originate from China and have some morphological differences from typical Japanese ones. In addition, we used sequences from the international GenBank database. According to the results of the analysis of ITS sequences, the M. basjoo samples form a single clade with M. itinerans and M. tonkinensis, possibly corresponding to the subsection in the section Musa. At the same time, M. basjoo from Peter the Great Botanical Garden differs in the primary sequence of the ITS1-5.8S rRNA-ITS2 from Japanese one forming a lowly supported clade with M. tonkinensis. Two M. basjoo samples collected in China, whose sequences are taken from the GenBank database, fall into a separate subclade within M. basjoo clade, possibly being a special species from this affinity group. According to the trnL-trnF chloroplast sequences, most of the M. basjoo samples also fall into the clade with M. itinerans. However, one M. basjoo specimen from the Genbank database is monophyletic with M. acuminata from a completely different clade. Possibly, the affinity group of M. basjoo is a compound hybrid complex containing plants that differ in the composition of the maternal genome.