Objective This study investigates the genetic diversity, population structure, and genetic relationships of wild and cultivated Musa in Yunnan, providing a theoretical basis for germplasm innovation and breeding.

Method Forty-six wild and cultivated Musa germplasms from Yunnan were collected for an analysis. Using SNP markers, population structures of the germplasms as well as genetic diversity and phylogenetic relationships of the species were analyzed and compared.

Result A total of 81.78 million high-quality SNPs with an average sequencing depth of 35.95× per sample were obtained. They were genetically low in diversity, as the mean observed heterozygosity (Ho) of 0.00044, the expected heterozygosity (He) of 0.00279, the inbreeding coefficient (Fis) of 0.7913, and the polymorphism information content (PIC) of 0.00088 indicated. The wild Musa had significantly higher He than the landraces (P＜0.05). The 46 germplasms could be divided into 9 groups, with the domesticated Group 5 and Group 9 being genetically highly homogeneous, the wild Group 6, Group 3, and others differentiated significantly, and M. coccinea in Group 1 significantly isolated with the highest fixation index (Fst). Phylogenetically, the AAA-type cultivated germplasms were most closely related to the M. balbisiana complex, whereas ABB-type counterparts between M. acuminata and M. balbisiana.

Conclusion The genetic diversity of Musa germplasms found in Yunnan was generally low. The landraces could offer little basis for breeding applications. On the other hand, the wild accessions had relatively high variations, and M. coccinea was the one that could be of value for gene conservation and new variety breeding.