Abstract Background and Aims Kaempferia galanga is a medicinally and economically important species valued for its aromatic and therapeutic properties. However, a lack of knowledge about its genetic diversity, particularly in accessions from Myanmar, hinders varietal improvement, product authentication and conservation efforts. This study aimed to characterize this diversity using morpho-anatomical, cytological and chemical analyses. Moreover, clear links between these traits and in vitro somatic embryogenesis responses were also assessed towards conservation and further utilization of the species. Methods We characterized ten K. galanga accessions from Myanmar based on morpho-anatomy, DNA ploidy level and flavonoid composition, using K. parviflora as an outgroup. Subsequently, the differential responses of selected genotypes to indirect somatic embryogenesis were evaluated. Key Results The accessions clustered into three distinct morpho-chemo-cytotypes: (1) small-leaf, anthocyanin-lacking, pentaploid (5x); (2) big-leaf, anthocyanin-containing, tetraploid (4x); and (3) big-leaf, anthocyanin-lacking, pentaploid (5x). While rhizome flavonoid profiles were similar, leaf chemotypes were distinct. Based on these profiles, a representative from each of the two contrasting pentaploid groups (one big-leaf and one small-leaf) were successfully established in tissue culture. While the small-leaf accession regenerated earlier, its big-leaf counterpart demonstrated superior prolificacy through secondary somatic embryogenesis, producing more regenerants, including unique variegated plantlets with ornamental and breeding potential. Conclusions This study establishes the first integrative framework for identifying Myanmar K. galanga varieties and reveals clear genotype-specific responses in tissue culture. These findings provide a robust basis for varietal selection, herbal product authentication and the development of scalable micropropagation systems for conservation and commercial use.