Kaempferia species are aromatic perennial herbs belonging to the Zingiberaceae, that have been used as folk medicine in Thailand. Identification and classification of Kaempferia is difficult because of the synonymy and morphological similarity between species. In this study, Amplified Fragment Length Polymorphism (AFLP) technique was employed for determination of the phylogenetic relationships among nine Kaempferia species. Thirty primer combinations were screened and four primer combinations produced a total of distinct and reproducible 253 bands ranging from 56 to 70 bands with an average 63.25 bands per primer combination. Genetic distance based on AFLP band samplified using four primer combinations was calculated and the similarity index (SI)ranged from 0.0277–0.9375. A dendrogram was constructed using Unweighted Pair Group Method of the Arithmetic Average (UPGMA). The results from the cluster analysis showed the studied species could be divided into two main groups. The phylogenetic relationships were associated with the morphological characteristics. In conclusion, AFLP fingerprint is a useful technique for identification of Kaempferia species and is an ideal marker system for extended studies including all Kaempferia species for infrageneric classification.