Alpinia galanga is an important species cultivated as a culinary spice and is the type species of the genus. It is hence a member of sect. Alpinia subsect. Alpinia (with non-tubular bracteoles). However, molecular phylogenetic analyses suggest that A. galanga is closely related to A. nigra in sect. Allughas (with tubular bracteoles). This clade, which includes A. conchigera, is strongly supported with a bootstrap value (BS) of 100% and a decay index (DI) of >+6. These results are based on the internal transcribed spacer (ITS) region of the 18S–25S nuclear ribosomal DNA. The region (405–423bp) was sequenced from 17 accessions representing 16 taxa of Zingiberaceae, including 15 species of Alpinia and one outgroup. The sequence divergence ranged from 0.5 to 15.6% among the ingroup and from 10.1 to 13.3% between the ingroup and the outgroup. The results also strongly support the sister relationship of A. rafflesiana and A. javanica in section Allughas (BS=100%, DI=>+6), thus the whole section is paraphyletic. Section Alpinia subsect. Catimbium is monophyletic (BS=100%, DI=+5). On the other hand, sect. Alpinia subsect. Alpinia is paraphyletic (BS=100%, DI=>+6) with respect to sect. Alpinia subsect. Catimbium. The results from a phylogenetic analysis of a subset of the taxa using the spacer between trnL (UAA) 3′ exon and trnF (GAA) of chloroplast DNA confirmed the position of A. galanga in sect. Allughas. It appears that A. galanga has evolved within sect. Allughas and the absence of tubular bracteoles is a convergence with sect. Alpinia, possibly as a result of evolution under domestication.