Introduction: Kaempferia parviflora or black ginger is abundantly cultivated because its rhizomes contain methoxyflavones that have many pharmacological properties.K. parviflora can be divided into two types, based on morphological characteristics, but differences in their chemical compositions have never been explored.Objectives: This research aims to find chemical markers that can be used to differentiate between the two types of K. parviflora, the red-leaf and green-leaf types, by quantifying the amounts of methoxyflavones.Material and methods: K. parviflora samples were collected from 39 locations in Thailand. Their genetic diversity was assessed by a genotyping-by-sequencing (GBS) technique to construct the population structure. Their chemical compositions were analyzed by high performance liquid chromatography-photodiode array detection to determine the methoxyflavone contents. Results:The population structure based on >3,000 single nucleotide polymorphism (SNP) markers showed that the samples can be divided into two groups, which were consistent with the classification by leaf margin color (red-leaf and green-leaf types). HPLC analysis revealed 3,5,7,3 0 ,4 0 -pentamethoxyflavone (PMF), 5,7dimethoxyflavone (DMF), 5,7,4 0 -trimethoxyflavone (TMF), 3,5,7-trimethoxyflavone and 3,5,7,4 0 -tetramethoxyflavone as major methoxyflavones that can be used as chemical markers. The red-leaf type showed higher amounts of PMF, TMF and 3,5,7,4 0 -tetramethoxyflavone than the green-leaf type, while the green-leaf type showed higher amounts of DMF and 3,5,7-trimethoxyflavone than the red-leaf type. Conclusion:These results provide another approach to discriminate the two types of K. parviflora using chemical profiles alongside genetic and morphological analyses.Therefore, a specific type of K. parviflora can be selected over the other based on preferences for a certain methoxyflavone.