Comparative sequencing of the nuclear ribosomal Internal Transcribed Spacer (ITS) and the chloroplast matK coding and non-coding regions was used to examine the evolutionary relationships among 53 accessions representing 13 genera of the Zingiberaceae, including 31 accessions of Amomum (Alpinioideae). Phylogenetic analyses of the ITS and matK sequences alone and in combination using maximum parsimony methods produced a moderately supported topology within Alpinioideae. Our results indicated that Amomum as currently defined is polyphyletic with three major groups of species that do not correspond with any previously recognized sectional classification of the genus. Our analyses also identified Paramomum as sister to Elettariopsis, which are both embedded within one group of Amomum. The other two groups of Amomum share common ancestors with additional genera of the Alpinioideae. ITS and matK sequences provide new data for inferring relationships within Amomum and allow fresh interpretations of morphological characters (such as anther appendage and fruit type) that may be of value in future classifications.