Very little is known about the small, tropical, monogeneric monocotyledon family Lowiaceae within the order Zingiberales. The phylogenetic position of Lowiaceae within Zingiberales is unclear, as are relationships within its single genus Orchidantha, which includes at least 16 species. This paper presents a phylogenetic analysis of Zingiberales based on 613 parsimony informative characters of the plastid matK gene, the trnL-trnF region, the rps16 intron, and a conservative part of the nuclear ribosomal ITS region (part of the 18S, 5.8S, and 26S rDNA). The resulting single most parsimonious tree indicates that Lowiaceae is sister to all the remaining families of Zingiberales. An analysis of the family (14 species) based on a data set consisting of six plastid and nuclear DNA regions, includes the first use of a cam intron for estimating phylogeny. The results suggest that the nuclear calmodulin (cam) intron may be useful for other lower taxonomic level phylogenetic analyses. In the resulting tree all Bornean species of Orchidantha form a strongly supported monophyletic group. An equally strongly supported clade within the Bornean group contains the species distributed in Sabah (Malaysia) and Brunei. The species from mainland Asia form a poorly supported group because of the unclear position of Orchidantha chinensis. However, the four Malay Peninsula species with flowers possessing a white labellum form a strongly supported monophyletic group.